gff_juncs v1.0.13
---------------------------
Reading GFF file '/projects/NBL/reference_files/UCSC/all.gtf.gff3'...done.
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	4225	7502	0	-	.	ID=NR_028269;Parent=NR_028269;
Offending exons overlapped:
chr15	hg18_refGene	exon	100333859	100334330	0	+	.	ID=NR_028269.;Parent=NR_028269;
chr16	hg18_refGene	exon	4044	4511	0	-	.	ID=NR_028269.;Parent=NR_028269;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	24475	25944	0	-	.	ID=NR_026820;Parent=NR_026820;
Offending exons overlapped:
chr19	hg18_refGene	exon	28330	28690	0	-	.	ID=NR_026820.;Parent=NR_026820;
chr9	hg18_refGene	exon	24395	24957	0	-	.	ID=NR_026820.;Parent=NR_026820;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	24475	25944	0	-	.	ID=NR_026818;Parent=NR_026818;
Offending exons overlapped:
chr19	hg18_refGene	exon	28330	28690	0	-	.	ID=NR_026818.;Parent=NR_026818;
chr9	hg18_refGene	exon	24395	24957	0	-	.	ID=NR_026818.;Parent=NR_026818;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	24475	25944	0	-	.	ID=NR_026822;Parent=NR_026822;
Offending exons overlapped:
chr19	hg18_refGene	exon	28330	28690	0	-	.	ID=NR_026822.;Parent=NR_026822;
chr9	hg18_refGene	exon	24395	24957	0	-	.	ID=NR_026822.;Parent=NR_026822;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	556051	556128	0	-	.	ID=NR_031741;Parent=NR_031741;
Offending exons overlapped:
chr1	hg18_refGene	exon	556051	556128	0	-	.	ID=NR_031741.;Parent=NR_031741;
chrM	hg18_refGene	exon	5640	5716	0	-	.	ID=NR_031741.;Parent=NR_031741;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	1256589	1259707	0	+	.	ID=NM_152228;Parent=NM_152228;
Offending exons overlapped:
chr1	hg18_refGene	exon	1258749	1259707	0	+	.	ID=NM_152228.;Parent=NM_152228;
chr1_random	hg18_refGene	exon	266954	267144	0	+	.	ID=NM_152228.;Parent=NM_152228;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	1298973	1300443	0	-	.	ID=NM_001127229;Parent=NM_001127229;
Offending exons overlapped:
chr1	hg18_refGene	exon	1300240	1300443	0	-	.	ID=NM_001127229.;Parent=NM_001127229;
chr1_random	hg18_refGene	exon	384702	384905	0	+	.	ID=NM_001127229.;Parent=NM_001127229;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	1298974	1300425	0	-	.	ID=NM_001127230;Parent=NM_001127230;
Offending exons overlapped:
chr1	hg18_refGene	exon	1300318	1300425	0	-	.	ID=NM_001127230.;Parent=NM_001127230;
chr1_random	hg18_refGene	exon	384720	384827	0	+	.	ID=NM_001127230.;Parent=NM_001127230;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	24165526	24179408	0	-	.	ID=NM_006625;Parent=NM_006625;
Offending exons overlapped:
chr1	hg18_refGene	exon	24179268	24179408	0	-	.	ID=NM_006625.;Parent=NM_006625;
chr1_random	hg18_refGene	exon	1500604	1501878	0	-	.	ID=NM_006625.;Parent=NM_006625;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	24168160	24179408	0	-	.	ID=NM_054016;Parent=NM_054016;
Offending exons overlapped:
chr1	hg18_refGene	exon	24179268	24179408	0	-	.	ID=NM_054016.;Parent=NM_054016;
chr1_random	hg18_refGene	exon	1503241	1505601	0	-	.	ID=NM_054016.;Parent=NM_054016;
Error: bad transcript annotation:
chr1	hg18_refGene	mRNA	109434926	109441077	0	+	.	ID=NM_020141;Parent=NM_020141;
Offending exons overlapped:
chr1	hg18_refGene	exon	109438562	109441077	0	+	.	ID=NM_020141.;Parent=NM_020141;
chr1_random	hg18_refGene	exon	126732	126833	0	+	.	ID=NM_020141.;Parent=NM_020141;
Error: bad transcript annotation:
chr11	hg18_refGene	mRNA	116211679	116213548	0	-	.	ID=NM_000039;Parent=NM_000039;
Offending exons overlapped:
chr11	hg18_refGene	exon	116213531	116213548	0	-	.	ID=NM_000039.;Parent=NM_000039;
chr22_random	hg18_refGene	exon	13498	13515	0	+	.	ID=NM_000039.;Parent=NM_000039;
Error: bad transcript annotation:
chr15	hg18_refGene	mRNA	26297379	26310007	0	+	.	ID=NR_033351;Parent=NR_033351;
Offending exons overlapped:
chr15	hg18_refGene	exon	26307620	26310007	0	+	.	ID=NR_033351.;Parent=NR_033351;
chr15_random	hg18_refGene	exon	258225	258396	0	+	.	ID=NR_033351.;Parent=NR_033351;
Error: bad transcript annotation:
chr15	hg18_refGene	mRNA	26297379	26310766	0	+	.	ID=NR_033353;Parent=NR_033353;
Offending exons overlapped:
chr15	hg18_refGene	exon	26307620	26310766	0	+	.	ID=NR_033353.;Parent=NR_033353;
chr15_random	hg18_refGene	exon	258225	258396	0	+	.	ID=NR_033353.;Parent=NR_033353;
Error: bad transcript annotation:
chr15	hg18_refGene	mRNA	80551134	80585378	0	-	.	ID=NR_026811;Parent=NR_026811;
Offending exons overlapped:
chr15	hg18_refGene	exon	80585121	80585378	0	-	.	ID=NR_026811.;Parent=NR_026811;
chr15_random	hg18_refGene	exon	427792	428049	0	+	.	ID=NR_026811.;Parent=NR_026811;
Error: bad transcript annotation:
chr16	hg18_refGene	mRNA	29661287	29664841	0	-	.	ID=NM_175900;Parent=NM_175900;
Offending exons overlapped:
chr16	hg18_refGene	exon	29664733	29664841	0	-	.	ID=NM_175900.;Parent=NM_175900;
chr16_random	hg18_refGene	exon	41078	43567	0	-	.	ID=NM_175900.;Parent=NM_175900;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	31517174	31528101	0	-	.	ID=NM_001001417;Parent=NM_001001417;
Offending exons overlapped:
chr17	hg18_refGene	exon	31527953	31528101	0	-	.	ID=NM_001001417.;Parent=NM_001001417;
chr17_random	hg18_refGene	exon	1292789	1292937	0	+	.	ID=NM_001001417.;Parent=NM_001001417;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	31546382	31548260	0	-	.	ID=NM_001001437;Parent=NM_001001437;
Offending exons overlapped:
chr17	hg18_refGene	exon	31548110	31548260	0	-	.	ID=NM_001001437.;Parent=NM_001001437;
chr17_random	hg18_refGene	exon	1225929	1226436	0	-	.	ID=NM_001001437.;Parent=NM_001001437;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	31546382	31548269	0	-	.	ID=NM_021006;Parent=NM_021006;
Offending exons overlapped:
chr17	hg18_refGene	exon	31548110	31548269	0	-	.	ID=NM_021006.;Parent=NM_021006;
chr17_random	hg18_refGene	exon	1225929	1226436	0	-	.	ID=NM_021006.;Parent=NM_021006;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	31562581	31564387	0	+	.	ID=NM_207007;Parent=NM_207007;
Offending exons overlapped:
chr17	hg18_refGene	exon	31563997	31564387	0	+	.	ID=NM_207007.;Parent=NM_207007;
chr17_random	hg18_refGene	exon	1242110	1242261	0	+	.	ID=NM_207007.;Parent=NM_207007;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	31562581	31564387	0	+	.	ID=NM_001001435;Parent=NM_001001435;
Offending exons overlapped:
chr17	hg18_refGene	exon	31563997	31564387	0	+	.	ID=NM_001001435.;Parent=NM_001001435;
chr17_random	hg18_refGene	exon	1242110	1242261	0	+	.	ID=NM_001001435.;Parent=NM_001001435;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	31605198	31616140	0	-	.	ID=NM_001001418;Parent=NM_001001418;
Offending exons overlapped:
chr17	hg18_refGene	exon	31615997	31616140	0	-	.	ID=NM_001001418.;Parent=NM_001001418;
chr17_random	hg18_refGene	exon	993948	994831	0	-	.	ID=NM_001001418.;Parent=NM_001001418;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	31605199	31616152	0	-	.	ID=NM_032258;Parent=NM_032258;
Offending exons overlapped:
chr17	hg18_refGene	exon	31615997	31616152	0	-	.	ID=NM_032258.;Parent=NM_032258;
chr17_random	hg18_refGene	exon	993949	994831	0	-	.	ID=NM_032258.;Parent=NM_032258;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	33541108	33552247	0	-	.	ID=NM_001123391;Parent=NM_001123391;
Offending exons overlapped:
chr17	hg18_refGene	exon	33552092	33552247	0	-	.	ID=NM_001123391.;Parent=NM_001123391;
chr17_random	hg18_refGene	exon	993765	994831	0	-	.	ID=NM_001123391.;Parent=NM_001123391;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36368195	36376670	0	-	.	ID=NM_213656;Parent=NM_213656;
Offending exons overlapped:
chr17	hg18_refGene	exon	36376167	36376670	0	-	.	ID=NM_213656.;Parent=NM_213656;
chr17_random	hg18_refGene	exon	386433	386936	0	+	.	ID=NM_213656.;Parent=NM_213656;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36387494	36396913	0	-	.	ID=NM_182497;Parent=NM_182497;
Offending exons overlapped:
chr17	hg18_refGene	exon	36396825	36396913	0	-	.	ID=NM_182497.;Parent=NM_182497;
chr17_random	hg18_refGene	exon	366190	366278	0	+	.	ID=NM_182497.;Parent=NM_182497;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36403208	36403911	0	-	.	ID=NM_033185;Parent=NM_033185;
Offending exons overlapped:
chr17	hg18_refGene	exon	36403208	36403911	0	-	.	ID=NM_033185.;Parent=NM_033185;
chr17_random	hg18_refGene	exon	359192	359895	0	+	.	ID=NM_033185.;Parent=NM_033185;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36408971	36409664	0	-	.	ID=NM_031959;Parent=NM_031959;
Offending exons overlapped:
chr17	hg18_refGene	exon	36408971	36409664	0	-	.	ID=NM_031959.;Parent=NM_031959;
chr17_random	hg18_refGene	exon	353439	354132	0	+	.	ID=NM_031959.;Parent=NM_031959;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36418300	36418892	0	-	.	ID=NM_031958;Parent=NM_031958;
Offending exons overlapped:
chr17	hg18_refGene	exon	36418300	36418892	0	-	.	ID=NM_031958.;Parent=NM_031958;
chr17_random	hg18_refGene	exon	344211	344803	0	+	.	ID=NM_031958.;Parent=NM_031958;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36435805	36436980	0	-	.	ID=NM_031957;Parent=NM_031957;
Offending exons overlapped:
chr17	hg18_refGene	exon	36435805	36436980	0	-	.	ID=NM_031957.;Parent=NM_031957;
chr17_random	hg18_refGene	exon	326123	327298	0	+	.	ID=NM_031957.;Parent=NM_031957;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36443663	36444633	0	-	.	ID=NM_030966;Parent=NM_030966;
Offending exons overlapped:
chr17	hg18_refGene	exon	36443663	36444633	0	-	.	ID=NM_030966.;Parent=NM_030966;
chr17_random	hg18_refGene	exon	318470	319440	0	+	.	ID=NM_030966.;Parent=NM_030966;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36450337	36451239	0	-	.	ID=NM_030967;Parent=NM_030967;
Offending exons overlapped:
chr17	hg18_refGene	exon	36450337	36451239	0	-	.	ID=NM_030967.;Parent=NM_030967;
chr17_random	hg18_refGene	exon	311866	312768	0	+	.	ID=NM_030967.;Parent=NM_030967;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36456322	36457094	0	-	.	ID=NM_001123387;Parent=NM_001123387;
Offending exons overlapped:
chr17	hg18_refGene	exon	36456322	36457094	0	-	.	ID=NM_001123387.;Parent=NM_001123387;
chr17_random	hg18_refGene	exon	306011	306783	0	+	.	ID=NM_001123387.;Parent=NM_001123387;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36469021	36469870	0	-	.	ID=NM_001165252;Parent=NM_001165252;
Offending exons overlapped:
chr17	hg18_refGene	exon	36469021	36469870	0	-	.	ID=NM_001165252.;Parent=NM_001165252;
chr17_random	hg18_refGene	exon	293130	293979	0	+	.	ID=NM_001165252.;Parent=NM_001165252;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36474895	36475657	0	-	.	ID=NM_033184;Parent=NM_033184;
Offending exons overlapped:
chr17	hg18_refGene	exon	36474895	36475657	0	-	.	ID=NM_033184.;Parent=NM_033184;
chr17_random	hg18_refGene	exon	287343	288105	0	+	.	ID=NM_033184.;Parent=NM_033184;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36526962	36528132	0	-	.	ID=NM_033059;Parent=NM_033059;
Offending exons overlapped:
chr17	hg18_refGene	exon	36526962	36528132	0	-	.	ID=NM_033059.;Parent=NM_033059;
chr17_random	hg18_refGene	exon	234616	235786	0	+	.	ID=NM_033059.;Parent=NM_033059;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	36532871	36533945	0	-	.	ID=NM_031854;Parent=NM_031854;
Offending exons overlapped:
chr17	hg18_refGene	exon	36532871	36533945	0	-	.	ID=NM_031854.;Parent=NM_031854;
chr17_random	hg18_refGene	exon	228817	229891	0	+	.	ID=NM_031854.;Parent=NM_031854;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	38719420	38727115	0	+	.	ID=NM_145041;Parent=NM_145041;
Offending exons overlapped:
chr17	hg18_refGene	exon	38725226	38727115	0	+	.	ID=NM_145041.;Parent=NM_145041;
chr17_random	hg18_refGene	exon	481040	481087	0	+	.	ID=NM_145041.;Parent=NM_145041;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	63462310	63473432	0	+	.	ID=NM_002266;Parent=NM_002266;
Offending exons overlapped:
chr17	hg18_refGene	exon	63473082	63473432	0	+	.	ID=NM_002266.;Parent=NM_002266;
chr17_random	hg18_refGene	exon	1713111	1713461	0	-	.	ID=NM_002266.;Parent=NM_002266;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77394323	77411833	0	-	.	ID=NM_000918;Parent=NM_000918;
Offending exons overlapped:
chr17	hg18_refGene	exon	77411492	77411833	0	-	.	ID=NM_000918.;Parent=NM_000918;
chr17_random	hg18_refGene	exon	2360338	2361278	0	-	.	ID=NM_000918.;Parent=NM_000918;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77418887	77422079	0	-	.	ID=NM_001185077;Parent=NM_001185077;
Offending exons overlapped:
chr17	hg18_refGene	exon	77421801	77422079	0	-	.	ID=NM_001185077.;Parent=NM_001185077;
chr17_random	hg18_refGene	exon	2385030	2386390	0	-	.	ID=NM_001185077.;Parent=NM_001185077;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77442895	77451655	0	+	.	ID=NM_001002244;Parent=NM_001002244;
Offending exons overlapped:
chr17	hg18_refGene	exon	77451088	77451655	0	+	.	ID=NM_001002244.;Parent=NM_001002244;
chr17_random	hg18_refGene	exon	2409126	2409266	0	+	.	ID=NM_001002244.;Parent=NM_001002244;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77453364	77454072	0	+	.	ID=NM_148896;Parent=NM_148896;
Offending exons overlapped:
chr17	hg18_refGene	exon	77453788	77454072	0	+	.	ID=NM_148896.;Parent=NM_148896;
chr17_random	hg18_refGene	exon	2419654	2419984	0	+	.	ID=NM_148896.;Parent=NM_148896;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77454070	77462369	0	-	.	ID=NR_033683;Parent=NR_033683;
Offending exons overlapped:
chr17	hg18_refGene	exon	77462069	77462369	0	-	.	ID=NR_033683.;Parent=NR_033683;
chr17_random	hg18_refGene	exon	2420362	2422412	0	-	.	ID=NR_033683.;Parent=NR_033683;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77454070	77462369	0	-	.	ID=NR_033685;Parent=NR_033685;
Offending exons overlapped:
chr17	hg18_refGene	exon	77462069	77462369	0	-	.	ID=NR_033685.;Parent=NR_033685;
chr17_random	hg18_refGene	exon	2420362	2422412	0	-	.	ID=NR_033685.;Parent=NR_033685;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77454070	77462632	0	-	.	ID=NR_033681;Parent=NR_033681;
Offending exons overlapped:
chr17	hg18_refGene	exon	77462435	77462632	0	-	.	ID=NR_033681.;Parent=NR_033681;
chr17_random	hg18_refGene	exon	2420362	2422412	0	-	.	ID=NR_033681.;Parent=NR_033681;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77454070	77462632	0	-	.	ID=NM_002861;Parent=NM_002861;
Offending exons overlapped:
chr17	hg18_refGene	exon	77462435	77462632	0	-	.	ID=NM_002861.;Parent=NM_002861;
chr17_random	hg18_refGene	exon	2420362	2422412	0	-	.	ID=NM_002861.;Parent=NM_002861;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77454070	77462632	0	-	.	ID=NR_033682;Parent=NR_033682;
Offending exons overlapped:
chr17	hg18_refGene	exon	77462435	77462632	0	-	.	ID=NR_033682.;Parent=NR_033682;
chr17_random	hg18_refGene	exon	2420362	2422412	0	-	.	ID=NR_033682.;Parent=NR_033682;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77454070	77462632	0	-	.	ID=NM_001184917;Parent=NM_001184917;
Offending exons overlapped:
chr17	hg18_refGene	exon	77462435	77462632	0	-	.	ID=NM_001184917.;Parent=NM_001184917;
chr17_random	hg18_refGene	exon	2420362	2422412	0	-	.	ID=NM_001184917.;Parent=NM_001184917;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77463107	77469332	0	-	.	ID=NM_016538;Parent=NM_016538;
Offending exons overlapped:
chr17	hg18_refGene	exon	77469207	77469332	0	-	.	ID=NM_016538.;Parent=NM_016538;
chr17_random	hg18_refGene	exon	2429448	2430126	0	-	.	ID=NM_016538.;Parent=NM_016538;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77469438	77474701	0	-	.	ID=NM_032711;Parent=NM_032711;
Offending exons overlapped:
chr17	hg18_refGene	exon	77474522	77474701	0	-	.	ID=NM_032711.;Parent=NM_032711;
chr17_random	hg18_refGene	exon	2435810	2440622	0	-	.	ID=NM_032711.;Parent=NM_032711;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77478996	77481919	0	+	.	ID=NR_015454;Parent=NR_015454;
Offending exons overlapped:
chr17	hg18_refGene	exon	77480643	77481919	0	+	.	ID=NR_015454.;Parent=NR_015454;
chr17_random	hg18_refGene	exon	2303452	2304068	0	+	.	ID=NR_015454.;Parent=NR_015454;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77483558	77488259	0	-	.	ID=NM_153824;Parent=NM_153824;
Offending exons overlapped:
chr17	hg18_refGene	exon	77487915	77488259	0	-	.	ID=NM_153824.;Parent=NM_153824;
chr17_random	hg18_refGene	exon	2308041	2308614	0	-	.	ID=NM_153824.;Parent=NM_153824;
Error: bad transcript annotation:
chr17	hg18_refGene	mRNA	77483560	77488259	0	-	.	ID=NM_006907;Parent=NM_006907;
Offending exons overlapped:
chr17	hg18_refGene	exon	77487915	77488259	0	-	.	ID=NM_006907.;Parent=NM_006907;
chr17_random	hg18_refGene	exon	2308043	2309031	0	-	.	ID=NM_006907.;Parent=NM_006907;
Error: bad transcript annotation:
chr19	hg18_refGene	mRNA	59927813	60001550	0	+	.	ID=NM_001015070;Parent=NM_001015070;
Offending exons overlapped:
chr19	hg18_refGene	exon	60001207	60001550	0	+	.	ID=NM_001015070.;Parent=NM_001015070;
chr19_random	hg18_refGene	exon	181168	181202	0	+	.	ID=NM_001015070.;Parent=NM_001015070;
Error: bad transcript annotation:
chr19	hg18_refGene	mRNA	60006879	60017784	0	+	.	ID=NM_001080772;Parent=NM_001080772;
Offending exons overlapped:
chr19	hg18_refGene	exon	60017109	60017784	0	+	.	ID=NM_001080772.;Parent=NM_001080772;
chr19_random	hg18_refGene	exon	199898	199977	0	+	.	ID=NM_001080772.;Parent=NM_001080772;
Error: bad transcript annotation:
chr19	hg18_refGene	mRNA	60006879	60017784	0	+	.	ID=NM_002255;Parent=NM_002255;
Offending exons overlapped:
chr19	hg18_refGene	exon	60017109	60017784	0	+	.	ID=NM_002255.;Parent=NM_002255;
chr19_random	hg18_refGene	exon	199898	199977	0	+	.	ID=NM_002255.;Parent=NM_002255;
Error: bad transcript annotation:
chr19	hg18_refGene	mRNA	60006879	60017784	0	+	.	ID=NM_001080770;Parent=NM_001080770;
Offending exons overlapped:
chr19	hg18_refGene	exon	60017109	60017784	0	+	.	ID=NM_001080770.;Parent=NM_001080770;
chr19_random	hg18_refGene	exon	199898	199977	0	+	.	ID=NM_001080770.;Parent=NM_001080770;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	149355836	149355887	0	-	.	ID=NR_031742;Parent=NR_031742;
Offending exons overlapped:
chr2	hg18_refGene	exon	149355836	149355887	0	-	.	ID=NR_031742.;Parent=NR_031742;
chrM	hg18_refGene	exon	622	673	0	+	.	ID=NR_031742.;Parent=NR_031742;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	242172494	242205589	0	-	.	ID=NM_001164356;Parent=NM_001164356;
Offending exons overlapped:
chr2	hg18_refGene	exon	242205500	242205589	0	-	.	ID=NM_001164356.;Parent=NM_001164356;
chr2_random	hg18_refGene	exon	1617	1936	0	-	.	ID=NM_001164356.;Parent=NM_001164356;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	242172494	242225398	0	-	.	ID=NM_015963;Parent=NM_015963;
Offending exons overlapped:
chr2	hg18_refGene	exon	242225029	242225398	0	-	.	ID=NM_015963.;Parent=NM_015963;
chr2_random	hg18_refGene	exon	1617	1936	0	-	.	ID=NM_015963.;Parent=NM_015963;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	242225700	242261944	0	+	.	ID=NM_013325;Parent=NM_013325;
Offending exons overlapped:
chr2	hg18_refGene	exon	242260279	242261944	0	+	.	ID=NM_013325.;Parent=NM_013325;
chr2_random	hg18_refGene	exon	54822	54934	0	+	.	ID=NM_013325.;Parent=NM_013325;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	242225700	242261944	0	+	.	ID=NM_178326;Parent=NM_178326;
Offending exons overlapped:
chr2	hg18_refGene	exon	242260279	242261944	0	+	.	ID=NM_178326.;Parent=NM_178326;
chr2_random	hg18_refGene	exon	54822	54934	0	+	.	ID=NM_178326.;Parent=NM_178326;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	242263830	242275056	0	-	.	ID=NR_033255;Parent=NR_033255;
Offending exons overlapped:
chr2	hg18_refGene	exon	242274742	242275056	0	-	.	ID=NR_033255.;Parent=NR_033255;
chr2_random	hg18_refGene	exon	92953	93448	0	-	.	ID=NR_033255.;Parent=NR_033255;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	242263830	242275056	0	-	.	ID=NM_001165031;Parent=NM_001165031;
Offending exons overlapped:
chr2	hg18_refGene	exon	242274742	242275056	0	-	.	ID=NM_001165031.;Parent=NM_001165031;
chr2_random	hg18_refGene	exon	92953	93448	0	-	.	ID=NM_001165031.;Parent=NM_001165031;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	242263830	242275056	0	-	.	ID=NM_012145;Parent=NM_012145;
Offending exons overlapped:
chr2	hg18_refGene	exon	242274742	242275056	0	-	.	ID=NM_012145.;Parent=NM_012145;
chr2_random	hg18_refGene	exon	92953	93448	0	-	.	ID=NM_012145.;Parent=NM_012145;
Error: bad transcript annotation:
chr2	hg18_refGene	mRNA	242322703	242356904	0	+	.	ID=NM_152783;Parent=NM_152783;
Offending exons overlapped:
chr2	hg18_refGene	exon	242355798	242356904	0	+	.	ID=NM_152783.;Parent=NM_152783;
chr2_random	hg18_refGene	exon	151162	151242	0	+	.	ID=NM_152783.;Parent=NM_152783;
Error: bad transcript annotation:
chr22	hg18_refGene	mRNA	40885963	40941389	0	-	.	ID=NM_181492;Parent=NM_181492;
Offending exons overlapped:
chr22	hg18_refGene	exon	40935601	40941389	0	-	.	ID=NM_181492.;Parent=NM_181492;
chr22_h2_hap1	hg18_refGene	exon	10697	16485	0	-	.	ID=NM_181492.;Parent=NM_181492;
Error: bad transcript annotation:
chr22	hg18_refGene	mRNA	40885963	40941389	0	-	.	ID=NM_005650;Parent=NM_005650;
Offending exons overlapped:
chr22	hg18_refGene	exon	40935601	40941389	0	-	.	ID=NM_005650.;Parent=NM_005650;
chr22_h2_hap1	hg18_refGene	exon	10697	16485	0	-	.	ID=NM_005650.;Parent=NM_005650;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	46370239	46375872	0	+	.	ID=NM_001123396;Parent=NM_001123396;
Offending exons overlapped:
chr3	hg18_refGene	exon	46373972	46375872	0	+	.	ID=NM_001123396.;Parent=NM_001123396;
chr3_random	hg18_refGene	exon	648511	648944	0	+	.	ID=NM_001123396.;Parent=NM_001123396;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	46370239	46377417	0	+	.	ID=NM_001123041;Parent=NM_001123041;
Offending exons overlapped:
chr3	hg18_refGene	exon	46376172	46377417	0	+	.	ID=NM_001123041.;Parent=NM_001123041;
chr3_random	hg18_refGene	exon	648511	648944	0	+	.	ID=NM_001123041.;Parent=NM_001123041;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	46386637	46392701	0	+	.	ID=NM_000579;Parent=NM_000579;
Offending exons overlapped:
chr3	hg18_refGene	exon	46389387	46392701	0	+	.	ID=NM_000579.;Parent=NM_000579;
chr3_random	hg18_refGene	exon	664915	664971	0	+	.	ID=NM_000579.;Parent=NM_000579;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	46386637	46392701	0	+	.	ID=NM_001100168;Parent=NM_001100168;
Offending exons overlapped:
chr3	hg18_refGene	exon	46389387	46392701	0	+	.	ID=NM_001100168.;Parent=NM_001100168;
chr3_random	hg18_refGene	exon	664915	664971	0	+	.	ID=NM_001100168.;Parent=NM_001100168;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	46423725	46426018	0	+	.	ID=NM_003965;Parent=NM_003965;
Offending exons overlapped:
chr3	hg18_refGene	exon	46424563	46426018	0	+	.	ID=NM_003965.;Parent=NM_003965;
chr3_random	hg18_refGene	exon	701980	702252	0	+	.	ID=NM_003965.;Parent=NM_003965;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	46424053	46426017	0	+	.	ID=NM_001130910;Parent=NM_001130910;
Offending exons overlapped:
chr3	hg18_refGene	exon	46424563	46426017	0	+	.	ID=NM_001130910.;Parent=NM_001130910;
chr3_random	hg18_refGene	exon	702308	702444	0	+	.	ID=NM_001130910.;Parent=NM_001130910;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	121797818	121803948	0	+	.	ID=NM_004547;Parent=NM_004547;
Offending exons overlapped:
chr3	hg18_refGene	exon	121803745	121803948	0	+	.	ID=NM_004547.;Parent=NM_004547;
chr3_random	hg18_refGene	exon	99127	99330	0	-	.	ID=NM_004547.;Parent=NM_004547;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	121797818	121803948	0	+	.	ID=NM_001168331;Parent=NM_001168331;
Offending exons overlapped:
chr3	hg18_refGene	exon	121802648	121803948	0	+	.	ID=NM_001168331.;Parent=NM_001168331;
chr3_random	hg18_refGene	exon	99127	100427	0	-	.	ID=NM_001168331.;Parent=NM_001168331;
Error: bad transcript annotation:
chr3	hg18_refGene	mRNA	121829706	121884108	0	-	.	ID=NM_000187;Parent=NM_000187;
Offending exons overlapped:
chr3	hg18_refGene	exon	121883634	121884108	0	-	.	ID=NM_000187.;Parent=NM_000187;
chr3_random	hg18_refGene	exon	18898	19372	0	+	.	ID=NM_000187.;Parent=NM_000187;
Error: bad transcript annotation:
chr4	hg18_refGene	mRNA	91978665	91979292	0	-	.	ID=NM_183049;Parent=NM_183049;
Offending exons overlapped:
chr4	hg18_refGene	exon	91978665	91979292	0	-	.	ID=NM_183049.;Parent=NM_183049;
chrX	hg18_refGene	exon	12903146	12903208	0	+	.	ID=NM_183049.;Parent=NM_183049;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68521131	68541940	0	+	.	ID=NM_022909;Parent=NM_022909;
Offending exons overlapped:
chr5	hg18_refGene	exon	68541290	68541940	0	+	.	ID=NM_022909.;Parent=NM_022909;
chr5_h2_hap1	hg18_refGene	exon	282	935	0	+	.	ID=NM_022909.;Parent=NM_022909;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68549329	68561741	0	+	.	ID=NM_033281;Parent=NM_033281;
Offending exons overlapped:
chr5	hg18_refGene	exon	68560791	68561741	0	+	.	ID=NM_033281.;Parent=NM_033281;
chr5_h2_hap1	hg18_refGene	exon	8324	8449	0	+	.	ID=NM_033281.;Parent=NM_033281;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68566378	68609013	0	+	.	ID=NM_001799;Parent=NM_001799;
Offending exons overlapped:
chr5	hg18_refGene	exon	68608690	68609013	0	+	.	ID=NM_001799.;Parent=NM_001799;
chr5_h2_hap1	hg18_refGene	exon	25371	25617	0	+	.	ID=NM_001799.;Parent=NM_001799;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68612275	68652166	0	-	.	ID=NM_176816;Parent=NM_176816;
Offending exons overlapped:
chr5	hg18_refGene	exon	68651820	68652166	0	-	.	ID=NM_176816.;Parent=NM_176816;
chr5_h2_hap1	hg18_refGene	exon	71263	73606	0	-	.	ID=NM_176816.;Parent=NM_176816;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68683309	68701165	0	-	.	ID=NM_016283;Parent=NM_016283;
Offending exons overlapped:
chr5	hg18_refGene	exon	68701046	68701165	0	-	.	ID=NM_016283.;Parent=NM_016283;
chr5_h2_hap1	hg18_refGene	exon	142315	142842	0	-	.	ID=NM_016283.;Parent=NM_016283;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68683309	68701596	0	-	.	ID=NM_001015891;Parent=NM_001015891;
Offending exons overlapped:
chr5	hg18_refGene	exon	68701240	68701596	0	-	.	ID=NM_001015891.;Parent=NM_001015891;
chr5_h2_hap1	hg18_refGene	exon	142315	142842	0	-	.	ID=NM_001015891.;Parent=NM_001015891;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68696326	68701165	0	-	.	ID=NM_003187;Parent=NM_003187;
Offending exons overlapped:
chr5	hg18_refGene	exon	68701046	68701165	0	-	.	ID=NM_003187.;Parent=NM_003187;
chr5_h2_hap1	hg18_refGene	exon	155334	156345	0	-	.	ID=NM_003187.;Parent=NM_003187;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68696326	68701596	0	-	.	ID=NM_001015892;Parent=NM_001015892;
Offending exons overlapped:
chr5	hg18_refGene	exon	68701240	68701596	0	-	.	ID=NM_001015892.;Parent=NM_001015892;
chr5_h2_hap1	hg18_refGene	exon	155334	156345	0	-	.	ID=NM_001015892.;Parent=NM_001015892;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68700880	68746387	0	+	.	ID=NM_133343;Parent=NM_133343;
Offending exons overlapped:
chr5	hg18_refGene	exon	68745614	68746387	0	+	.	ID=NM_133343.;Parent=NM_133343;
chr5_h2_hap1	hg18_refGene	exon	159889	160056	0	+	.	ID=NM_133343.;Parent=NM_133343;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68701395	68746387	0	+	.	ID=NM_133338;Parent=NM_133338;
Offending exons overlapped:
chr5	hg18_refGene	exon	68745614	68746387	0	+	.	ID=NM_133338.;Parent=NM_133338;
chr5_h2_hap1	hg18_refGene	exon	160404	160525	0	+	.	ID=NM_133338.;Parent=NM_133338;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68701395	68746387	0	+	.	ID=NM_133344;Parent=NM_133344;
Offending exons overlapped:
chr5	hg18_refGene	exon	68745614	68746387	0	+	.	ID=NM_133344.;Parent=NM_133344;
chr5_h2_hap1	hg18_refGene	exon	160404	160525	0	+	.	ID=NM_133344.;Parent=NM_133344;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68701395	68746387	0	+	.	ID=NM_133342;Parent=NM_133342;
Offending exons overlapped:
chr5	hg18_refGene	exon	68745614	68746387	0	+	.	ID=NM_133342.;Parent=NM_133342;
chr5_h2_hap1	hg18_refGene	exon	160404	160525	0	+	.	ID=NM_133342.;Parent=NM_133342;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68702288	68746384	0	+	.	ID=NM_002873;Parent=NM_002873;
Offending exons overlapped:
chr5	hg18_refGene	exon	68745614	68746384	0	+	.	ID=NM_002873.;Parent=NM_002873;
chr5_h2_hap1	hg18_refGene	exon	161297	161763	0	+	.	ID=NM_002873.;Parent=NM_002873;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68702618	68746387	0	+	.	ID=NM_133340;Parent=NM_133340;
Offending exons overlapped:
chr5	hg18_refGene	exon	68745614	68746387	0	+	.	ID=NM_133340.;Parent=NM_133340;
chr5_h2_hap1	hg18_refGene	exon	161627	161763	0	+	.	ID=NM_133340.;Parent=NM_133340;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68702618	68746387	0	+	.	ID=NM_133341;Parent=NM_133341;
Offending exons overlapped:
chr5	hg18_refGene	exon	68745614	68746387	0	+	.	ID=NM_133341.;Parent=NM_133341;
chr5_h2_hap1	hg18_refGene	exon	161627	161763	0	+	.	ID=NM_133341.;Parent=NM_133341;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68703037	68746387	0	+	.	ID=NM_133339;Parent=NM_133339;
Offending exons overlapped:
chr5	hg18_refGene	exon	68745614	68746387	0	+	.	ID=NM_133339.;Parent=NM_133339;
chr5_h2_hap1	hg18_refGene	exon	162043	162146	0	+	.	ID=NM_133339.;Parent=NM_133339;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68713443	69917303	0	-	.	ID=NR_029426_dup1;Parent=NR_029426;
Offending exons overlapped:
chr5	hg18_refGene	exon	69917202	69917303	0	-	.	ID=NR_029426_dup1.;Parent=NR_029426_dup1;
chr5_h2_hap1	hg18_refGene	exon	1076824	1077681	0	-	.	ID=NR_029426_dup1.;Parent=NR_029426_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68746695	68773644	0	+	.	ID=NM_001038603;Parent=NM_001038603;
Offending exons overlapped:
chr5	hg18_refGene	exon	68773115	68773644	0	+	.	ID=NM_001038603.;Parent=NM_001038603;
chr5_h2_hap1	hg18_refGene	exon	205931	205989	0	+	.	ID=NM_001038603.;Parent=NM_001038603;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68823875	68885889	0	+	.	ID=NM_002538;Parent=NM_002538;
Offending exons overlapped:
chr5	hg18_refGene	exon	68885153	68885889	0	+	.	ID=NM_002538.;Parent=NM_002538;
chr5_h2_hap1	hg18_refGene	exon	282585	282952	0	+	.	ID=NM_002538.;Parent=NM_002538;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68866399	68885276	0	+	.	ID=NR_026578;Parent=NR_026578;
Offending exons overlapped:
chr5	hg18_refGene	exon	68885153	68885276	0	+	.	ID=NR_026578.;Parent=NR_026578;
chr5_h2_hap1	hg18_refGene	exon	325156	325179	0	+	.	ID=NR_026578.;Parent=NR_026578;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68891806	68926810	0	+	.	ID=NR_033417;Parent=NR_033417;
Offending exons overlapped:
chr5	hg18_refGene	exon	68926032	68926810	0	+	.	ID=NR_033417.;Parent=NR_033417;
chr5_h2_hap1	hg18_refGene	exon	350567	350747	0	+	.	ID=NR_033417.;Parent=NR_033417;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68891807	68924485	0	+	.	ID=NM_001098728;Parent=NM_001098728;
Offending exons overlapped:
chr5	hg18_refGene	exon	68923662	68924485	0	+	.	ID=NM_001098728.;Parent=NM_001098728;
chr5_h2_hap1	hg18_refGene	exon	350568	350747	0	+	.	ID=NM_001098728.;Parent=NM_001098728;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68891810	68924334	0	+	.	ID=NM_001515;Parent=NM_001515;
Offending exons overlapped:
chr5	hg18_refGene	exon	68923662	68924334	0	+	.	ID=NM_001515.;Parent=NM_001515;
chr5_h2_hap1	hg18_refGene	exon	350571	350747	0	+	.	ID=NM_001515.;Parent=NM_001515;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68891830	68924108	0	+	.	ID=NM_001042490;Parent=NM_001042490;
Offending exons overlapped:
chr5	hg18_refGene	exon	68923662	68924108	0	+	.	ID=NM_001042490.;Parent=NM_001042490;
chr5_h2_hap1	hg18_refGene	exon	350591	350747	0	+	.	ID=NM_001042490.;Parent=NM_001042490;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68962736	68964784	0	-	.	ID=NR_027439;Parent=NR_027439;
Offending exons overlapped:
chr5	hg18_refGene	exon	68962736	68964784	0	-	.	ID=NR_027439.;Parent=NR_027439;
chr5_h2_hap1	hg18_refGene	exon	639140	641188	0	-	.	ID=NR_027439.;Parent=NR_027439;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	68971046	69042028	0	-	.	ID=NR_027386;Parent=NR_027386;
Offending exons overlapped:
chr5	hg18_refGene	exon	69041927	69042028	0	-	.	ID=NR_027386.;Parent=NR_027386;
chr5_h2_hap1	hg18_refGene	exon	646636	647539	0	-	.	ID=NR_027386.;Parent=NR_027386;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69356828	69364281	0	+	.	ID=NM_022968;Parent=NM_022968;
Offending exons overlapped:
chr5	hg18_refGene	exon	69363898	69364281	0	+	.	ID=NM_022968.;Parent=NM_022968;
chr5_h2_hap1	hg18_refGene	exon	510080	510463	0	-	.	ID=NM_022968.;Parent=NM_022968;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69356828	69374695	0	+	.	ID=NM_021967;Parent=NM_021967;
Offending exons overlapped:
chr5	hg18_refGene	exon	69373107	69374695	0	+	.	ID=NM_021967.;Parent=NM_021967;
chr5_h2_hap1	hg18_refGene	exon	499653	501241	0	-	.	ID=NM_021967.;Parent=NM_021967;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69356834	69364278	0	+	.	ID=NM_001178087;Parent=NM_001178087;
Offending exons overlapped:
chr5	hg18_refGene	exon	69363898	69364278	0	+	.	ID=NM_001178087.;Parent=NM_001178087;
chr5_h2_hap1	hg18_refGene	exon	510082	510463	0	-	.	ID=NM_001178087.;Parent=NM_001178087;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69356834	69374688	0	+	.	ID=NM_022978;Parent=NM_022978;
Offending exons overlapped:
chr5	hg18_refGene	exon	69373107	69374688	0	+	.	ID=NM_022978.;Parent=NM_022978;
chr5_h2_hap1	hg18_refGene	exon	499660	501241	0	-	.	ID=NM_022978.;Parent=NM_022978;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69381106	69409172	0	+	.	ID=NM_022874;Parent=NM_022874;
Offending exons overlapped:
chr5	hg18_refGene	exon	69408602	69409172	0	+	.	ID=NM_022874.;Parent=NM_022874;
chr5_h2_hap1	hg18_refGene	exon	465178	465748	0	-	.	ID=NM_022874.;Parent=NM_022874;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69381106	69409172	0	+	.	ID=NM_000344;Parent=NM_000344;
Offending exons overlapped:
chr5	hg18_refGene	exon	69408602	69409172	0	+	.	ID=NM_000344.;Parent=NM_000344;
chr5_h2_hap1	hg18_refGene	exon	465178	465748	0	-	.	ID=NM_000344.;Parent=NM_000344;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69381106	69409177	0	+	.	ID=NM_022876;Parent=NM_022876;
Offending exons overlapped:
chr5	hg18_refGene	exon	69408602	69409177	0	+	.	ID=NM_022876.;Parent=NM_022876;
chr5_h2_hap1	hg18_refGene	exon	465173	465748	0	-	.	ID=NM_022876.;Parent=NM_022876;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69381106	69409177	0	+	.	ID=NM_022875;Parent=NM_022875;
Offending exons overlapped:
chr5	hg18_refGene	exon	69408602	69409177	0	+	.	ID=NM_022875.;Parent=NM_022875;
chr5_h2_hap1	hg18_refGene	exon	465173	465748	0	-	.	ID=NM_022875.;Parent=NM_022875;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69381106	69409177	0	+	.	ID=NM_017411;Parent=NM_017411;
Offending exons overlapped:
chr5	hg18_refGene	exon	69408602	69409177	0	+	.	ID=NM_017411.;Parent=NM_017411;
chr5_h2_hap1	hg18_refGene	exon	465173	465748	0	-	.	ID=NM_017411.;Parent=NM_017411;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69381106	69409177	0	+	.	ID=NM_022877;Parent=NM_022877;
Offending exons overlapped:
chr5	hg18_refGene	exon	69408602	69409177	0	+	.	ID=NM_022877.;Parent=NM_022877;
chr5_h2_hap1	hg18_refGene	exon	465173	465748	0	-	.	ID=NM_022877.;Parent=NM_022877;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69459045	69557378	0	-	.	ID=NR_024054;Parent=NR_024054;
Offending exons overlapped:
chr5	hg18_refGene	exon	69557191	69557378	0	-	.	ID=NR_024054.;Parent=NR_024054;
chr5_h2_hap1	hg18_refGene	exon	567287	567401	0	-	.	ID=NR_024054.;Parent=NR_024054;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69470446	69621760	0	-	.	ID=NR_029426;Parent=NR_029426;
Offending exons overlapped:
chr5	hg18_refGene	exon	69621659	69621760	0	-	.	ID=NR_029426.;Parent=NR_029426;
chr5_h2_hap1	hg18_refGene	exon	563819	564675	0	-	.	ID=NR_029426.;Parent=NR_029426;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69746953	69781944	0	+	.	ID=NR_033417_dup1;Parent=NR_033417;
Offending exons overlapped:
chr5	hg18_refGene	exon	69778817	69781944	0	+	.	ID=NR_033417_dup1.;Parent=NR_033417_dup1;
chr5_h2_hap1	hg18_refGene	exon	970348	971096	0	-	.	ID=NR_033417_dup1.;Parent=NR_033417_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69746954	69779640	0	+	.	ID=NM_001098728_dup1;Parent=NM_001098728;
Offending exons overlapped:
chr5	hg18_refGene	exon	69778817	69779640	0	+	.	ID=NM_001098728_dup1.;Parent=NM_001098728_dup1;
chr5_h2_hap1	hg18_refGene	exon	972664	973487	0	-	.	ID=NM_001098728_dup1.;Parent=NM_001098728_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	69746977	69779263	0	+	.	ID=NM_001042490_dup1;Parent=NM_001042490;
Offending exons overlapped:
chr5	hg18_refGene	exon	69778817	69779263	0	+	.	ID=NM_001042490_dup1.;Parent=NM_001042490_dup1;
chr5_h2_hap1	hg18_refGene	exon	973041	973487	0	-	.	ID=NM_001042490_dup1.;Parent=NM_001042490_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70300066	70356697	0	-	.	ID=NM_022892;Parent=NM_022892;
Offending exons overlapped:
chr5	hg18_refGene	exon	70356198	70356697	0	-	.	ID=NM_022892.;Parent=NM_022892;
chr5_h2_hap1	hg18_refGene	exon	393128	393627	0	+	.	ID=NM_022892.;Parent=NM_022892;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70300066	70356697	0	-	.	ID=NM_004536;Parent=NM_004536;
Offending exons overlapped:
chr5	hg18_refGene	exon	70356198	70356697	0	-	.	ID=NM_004536.;Parent=NM_004536;
chr5_h2_hap1	hg18_refGene	exon	393128	393627	0	+	.	ID=NM_004536.;Parent=NM_004536;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70366707	70399253	0	-	.	ID=NM_001515_dup1;Parent=NM_001515;
Offending exons overlapped:
chr5	hg18_refGene	exon	70399077	70399253	0	-	.	ID=NM_001515_dup1.;Parent=NM_001515_dup1;
chr5_h2_hap1	hg18_refGene	exon	972815	973487	0	-	.	ID=NM_001515_dup1.;Parent=NM_001515_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70405175	70424776	0	-	.	ID=NM_002538_dup1;Parent=NM_002538;
Offending exons overlapped:
chr5	hg18_refGene	exon	70424630	70424776	0	-	.	ID=NM_002538_dup1.;Parent=NM_002538_dup1;
chr5_h2_hap1	hg18_refGene	exon	1011232	1011968	0	-	.	ID=NM_002538_dup1.;Parent=NM_002538_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70405786	70424653	0	-	.	ID=NR_026578_dup1;Parent=NR_026578;
Offending exons overlapped:
chr5	hg18_refGene	exon	70424630	70424653	0	-	.	ID=NR_026578_dup1.;Parent=NR_026578_dup1;
chr5_h2_hap1	hg18_refGene	exon	1011845	1011968	0	-	.	ID=NR_026578_dup1.;Parent=NR_026578_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70432839	70460336	0	-	.	ID=NM_004536_dup1;Parent=NM_004536;
Offending exons overlapped:
chr5	hg18_refGene	exon	70460255	70460336	0	-	.	ID=NM_004536_dup1.;Parent=NM_004536_dup1;
chr5_h2_hap1	hg18_refGene	exon	1038916	1040044	0	-	.	ID=NM_004536_dup1.;Parent=NM_004536_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70432839	70460339	0	-	.	ID=NM_022892_dup1;Parent=NM_022892;
Offending exons overlapped:
chr5	hg18_refGene	exon	70460255	70460339	0	-	.	ID=NM_022892_dup1.;Parent=NM_022892_dup1;
chr5_h2_hap1	hg18_refGene	exon	1038916	1040044	0	-	.	ID=NM_022892_dup1.;Parent=NM_022892_dup1;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70707368	70717576	0	+	.	ID=NR_003922;Parent=NR_003922;
Offending exons overlapped:
chr5	hg18_refGene	exon	70717399	70717576	0	+	.	ID=NR_003922.;Parent=NR_003922;
chr5_h2_hap1	hg18_refGene	exon	1332449	1332680	0	+	.	ID=NR_003922.;Parent=NR_003922;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70787198	70899405	0	+	.	ID=NM_018429;Parent=NM_018429;
Offending exons overlapped:
chr5	hg18_refGene	exon	70896337	70899405	0	+	.	ID=NM_018429.;Parent=NM_018429;
chr5_h2_hap1	hg18_refGene	exon	1412261	1412735	0	+	.	ID=NM_018429.;Parent=NM_018429;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	70918871	70990286	0	+	.	ID=NM_022132;Parent=NM_022132;
Offending exons overlapped:
chr5	hg18_refGene	exon	70988326	70990286	0	+	.	ID=NM_022132.;Parent=NM_022132;
chr5_h2_hap1	hg18_refGene	exon	1543934	1544200	0	+	.	ID=NM_022132.;Parent=NM_022132;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	71050746	71052631	0	+	.	ID=NM_004291;Parent=NM_004291;
Offending exons overlapped:
chr5	hg18_refGene	exon	71052091	71052631	0	+	.	ID=NM_004291.;Parent=NM_004291;
chr5_h2_hap1	hg18_refGene	exon	1675809	1676098	0	+	.	ID=NM_004291.;Parent=NM_004291;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	93930929	93930997	0	-	.	ID=NR_031738;Parent=NR_031738;
Offending exons overlapped:
chr5	hg18_refGene	exon	93930929	93930997	0	-	.	ID=NR_031738.;Parent=NR_031738;
chrM	hg18_refGene	exon	14675	14744	0	-	.	ID=NR_031738.;Parent=NR_031738;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	180207221	180220892	0	-	.	ID=NM_001172638;Parent=NM_001172638;
Offending exons overlapped:
chr5	hg18_refGene	exon	180220825	180220892	0	-	.	ID=NM_001172638.;Parent=NM_001172638;
chr5_random	hg18_refGene	exon	12671	16549	0	-	.	ID=NM_001172638.;Parent=NM_001172638;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	180207221	180220892	0	-	.	ID=NM_152283;Parent=NM_152283;
Offending exons overlapped:
chr5	hg18_refGene	exon	180220825	180220892	0	-	.	ID=NM_152283.;Parent=NM_152283;
chr5_random	hg18_refGene	exon	12671	16549	0	-	.	ID=NM_152283.;Parent=NM_152283;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	180258683	180310510	0	+	.	ID=NM_001040462;Parent=NM_001040462;
Offending exons overlapped:
chr5	hg18_refGene	exon	180309510	180310510	0	+	.	ID=NM_001040462.;Parent=NM_001040462;
chr5_random	hg18_refGene	exon	64107	64389	0	+	.	ID=NM_001040462.;Parent=NM_001040462;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	180258683	180310510	0	+	.	ID=NM_001159709;Parent=NM_001159709;
Offending exons overlapped:
chr5	hg18_refGene	exon	180309510	180310510	0	+	.	ID=NM_001159709.;Parent=NM_001159709;
chr5_random	hg18_refGene	exon	64107	64389	0	+	.	ID=NM_001159709.;Parent=NM_001159709;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	180258683	180310510	0	+	.	ID=NM_001159707;Parent=NM_001159707;
Offending exons overlapped:
chr5	hg18_refGene	exon	180309510	180310510	0	+	.	ID=NM_001159707.;Parent=NM_001159707;
chr5_random	hg18_refGene	exon	64107	64389	0	+	.	ID=NM_001159707.;Parent=NM_001159707;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	180258683	180310510	0	+	.	ID=NM_001159708;Parent=NM_001159708;
Offending exons overlapped:
chr5	hg18_refGene	exon	180309510	180310510	0	+	.	ID=NM_001159708.;Parent=NM_001159708;
chr5_random	hg18_refGene	exon	64107	64389	0	+	.	ID=NM_001159708.;Parent=NM_001159708;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	180258683	180310510	0	+	.	ID=NM_024850;Parent=NM_024850;
Offending exons overlapped:
chr5	hg18_refGene	exon	180309510	180310510	0	+	.	ID=NM_024850.;Parent=NM_024850;
chr5_random	hg18_refGene	exon	64107	64389	0	+	.	ID=NM_024850.;Parent=NM_024850;
Error: bad transcript annotation:
chr5	hg18_refGene	mRNA	180269170	180310510	0	+	.	ID=NM_001159710;Parent=NM_001159710;
Offending exons overlapped:
chr5	hg18_refGene	exon	180309510	180310510	0	+	.	ID=NM_001159710.;Parent=NM_001159710;
chr5_random	hg18_refGene	exon	74593	74726	0	+	.	ID=NM_001159710.;Parent=NM_001159710;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	28647386	28663091	0	-	.	ID=NM_052923;Parent=NM_052923;
Offending exons overlapped:
chr6	hg18_refGene	exon	28662054	28663091	0	-	.	ID=NM_052923.;Parent=NM_052923;
chr6_cox_hap1	hg18_refGene	exon	1	321	0	-	.	ID=NM_052923.;Parent=NM_052923;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	28935381	28939433	0	-	.	ID=NR_033379;Parent=NR_033379;
Offending exons overlapped:
chr6	hg18_refGene	exon	28939040	28939433	0	-	.	ID=NR_033379.;Parent=NR_033379;
chr6_cox_hap1	hg18_refGene	exon	286755	289140	0	-	.	ID=NR_033379.;Parent=NR_033379;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	28978758	28999747	0	-	.	ID=NM_006510;Parent=NM_006510;
Offending exons overlapped:
chr6	hg18_refGene	exon	28998969	28999747	0	-	.	ID=NM_006510.;Parent=NM_006510;
chr6_cox_hap1	hg18_refGene	exon	330310	331973	0	-	.	ID=NM_006510.;Parent=NM_006510;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29070573	29081016	0	-	.	ID=NM_001010877;Parent=NM_001010877;
Offending exons overlapped:
chr6	hg18_refGene	exon	29080764	29081016	0	-	.	ID=NM_001010877.;Parent=NM_001010877;
chr6_cox_hap1	hg18_refGene	exon	417900	419669	0	-	.	ID=NM_001010877.;Parent=NM_001010877;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29119969	29120931	0	-	.	ID=NM_030903;Parent=NM_030903;
Offending exons overlapped:
chr6	hg18_refGene	exon	29119969	29120931	0	-	.	ID=NM_030903.;Parent=NM_030903;
chr6_cox_hap1	hg18_refGene	exon	467314	468276	0	-	.	ID=NM_030903.;Parent=NM_030903;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29161964	29163069	0	-	.	ID=NM_001005226;Parent=NM_001005226;
Offending exons overlapped:
chr6	hg18_refGene	exon	29161964	29163069	0	-	.	ID=NM_001005226.;Parent=NM_001005226;
chr6_cox_hap1	hg18_refGene	exon	509366	510470	0	-	.	ID=NM_001005226.;Parent=NM_001005226;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29187647	29188582	0	+	.	ID=NM_001005216;Parent=NM_001005216;
Offending exons overlapped:
chr6	hg18_refGene	exon	29187647	29188582	0	+	.	ID=NM_001005216.;Parent=NM_001005216;
chr6_cox_hap1	hg18_refGene	exon	535052	535987	0	+	.	ID=NM_001005216.;Parent=NM_001005216;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29249290	29250330	0	+	.	ID=NM_030905;Parent=NM_030905;
Offending exons overlapped:
chr6	hg18_refGene	exon	29249290	29250330	0	+	.	ID=NM_030905.;Parent=NM_030905;
chr6_cox_hap1	hg18_refGene	exon	596690	597730	0	+	.	ID=NM_030905.;Parent=NM_030905;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29382446	29383411	0	+	.	ID=NM_030946;Parent=NM_030946;
Offending exons overlapped:
chr6	hg18_refGene	exon	29382446	29383411	0	+	.	ID=NM_030946.;Parent=NM_030946;
chr6_cox_hap1	hg18_refGene	exon	729893	730858	0	+	.	ID=NM_030946.;Parent=NM_030946;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29430986	29432033	0	-	.	ID=NM_030876;Parent=NM_030876;
Offending exons overlapped:
chr6	hg18_refGene	exon	29430986	29432033	0	-	.	ID=NM_030876.;Parent=NM_030876;
chr6_cox_hap1	hg18_refGene	exon	778433	779480	0	-	.	ID=NM_030876.;Parent=NM_030876;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29449179	29451047	0	-	.	ID=NM_030959;Parent=NM_030959;
Offending exons overlapped:
chr6	hg18_refGene	exon	29449179	29451047	0	-	.	ID=NM_030959.;Parent=NM_030959;
chr6_cox_hap1	hg18_refGene	exon	796641	798509	0	-	.	ID=NM_030959.;Parent=NM_030959;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29472395	29473427	0	+	.	ID=NM_013936;Parent=NM_013936;
Offending exons overlapped:
chr6	hg18_refGene	exon	29472395	29473427	0	+	.	ID=NM_013936.;Parent=NM_013936;
chr6_cox_hap1	hg18_refGene	exon	819713	820745	0	+	.	ID=NM_013936.;Parent=NM_013936;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29501260	29503488	0	-	.	ID=NM_013937;Parent=NM_013937;
Offending exons overlapped:
chr6	hg18_refGene	exon	29501260	29503488	0	-	.	ID=NM_013937.;Parent=NM_013937;
chr6_cox_hap1	hg18_refGene	exon	848566	850794	0	-	.	ID=NM_013937.;Parent=NM_013937;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29515772	29516710	0	+	.	ID=NM_013941;Parent=NM_013941;
Offending exons overlapped:
chr6	hg18_refGene	exon	29515772	29516710	0	+	.	ID=NM_013941.;Parent=NM_013941;
chr6_cox_hap1	hg18_refGene	exon	863078	864016	0	+	.	ID=NM_013941.;Parent=NM_013941;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29534209	29540078	0	+	.	ID=NM_030883;Parent=NM_030883;
Offending exons overlapped:
chr6	hg18_refGene	exon	29537251	29540078	0	+	.	ID=NM_030883.;Parent=NM_030883;
chr6_cox_hap1	hg18_refGene	exon	881519	881635	0	+	.	ID=NM_030883.;Parent=NM_030883;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29562522	29563658	0	-	.	ID=NM_052967;Parent=NM_052967;
Offending exons overlapped:
chr6	hg18_refGene	exon	29562522	29563658	0	-	.	ID=NM_052967.;Parent=NM_052967;
chr6_cox_hap1	hg18_refGene	exon	909831	910967	0	-	.	ID=NM_052967.;Parent=NM_052967;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29631369	29635681	0	-	.	ID=NM_006398;Parent=NM_006398;
Offending exons overlapped:
chr6	hg18_refGene	exon	29635431	29635681	0	-	.	ID=NM_006398.;Parent=NM_006398;
chr6_cox_hap1	hg18_refGene	exon	978707	979444	0	-	.	ID=NM_006398.;Parent=NM_006398;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29658008	29658084	0	+	.	ID=NR_003049;Parent=NR_003049;
Offending exons overlapped:
chr6	hg18_refGene	exon	29658008	29658084	0	+	.	ID=NR_003049.;Parent=NR_003049;
chr6_cox_hap1	hg18_refGene	exon	1005345	1005421	0	+	.	ID=NR_003049.;Parent=NR_003049;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29663662	29664724	0	+	.	ID=NM_007160;Parent=NM_007160;
Offending exons overlapped:
chr6	hg18_refGene	exon	29663662	29664724	0	+	.	ID=NM_007160.;Parent=NM_007160;
chr6_cox_hap1	hg18_refGene	exon	1010999	1012061	0	+	.	ID=NM_007160.;Parent=NM_007160;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29677984	29703984	0	-	.	ID=NM_021903;Parent=NM_021903;
Offending exons overlapped:
chr6	hg18_refGene	exon	29703242	29703984	0	-	.	ID=NM_021903.;Parent=NM_021903;
chr6_cox_hap1	hg18_refGene	exon	1025321	1026809	0	-	.	ID=NM_021903.;Parent=NM_021903;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29677984	29708941	0	-	.	ID=NM_001470;Parent=NM_001470;
Offending exons overlapped:
chr6	hg18_refGene	exon	29708606	29708941	0	-	.	ID=NM_001470.;Parent=NM_001470;
chr6_cox_hap1	hg18_refGene	exon	1025321	1026809	0	-	.	ID=NM_001470.;Parent=NM_001470;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29677984	29708941	0	-	.	ID=NM_021904;Parent=NM_021904;
Offending exons overlapped:
chr6	hg18_refGene	exon	29708606	29708941	0	-	.	ID=NM_021904.;Parent=NM_021904;
chr6_cox_hap1	hg18_refGene	exon	1025321	1026809	0	-	.	ID=NM_021904.;Parent=NM_021904;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_001008228;Parent=NM_001008228;
Offending exons overlapped:
chr6	hg18_refGene	exon	29746928	29748126	0	+	.	ID=NM_001008228.;Parent=NM_001008228;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_001008228.;Parent=NM_001008228;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_206814;Parent=NM_206814;
Offending exons overlapped:
chr6	hg18_refGene	exon	29746928	29748126	0	+	.	ID=NM_206814.;Parent=NM_206814;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_206814.;Parent=NM_206814;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_002433;Parent=NM_002433;
Offending exons overlapped:
chr6	hg18_refGene	exon	29747178	29748126	0	+	.	ID=NM_002433.;Parent=NM_002433;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_002433.;Parent=NM_002433;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_001008229;Parent=NM_001008229;
Offending exons overlapped:
chr6	hg18_refGene	exon	29747178	29748126	0	+	.	ID=NM_001008229.;Parent=NM_001008229;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_001008229.;Parent=NM_001008229;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_206810;Parent=NM_206810;
Offending exons overlapped:
chr6	hg18_refGene	exon	29747178	29748126	0	+	.	ID=NM_206810.;Parent=NM_206810;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_206810.;Parent=NM_206810;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_206813;Parent=NM_206813;
Offending exons overlapped:
chr6	hg18_refGene	exon	29747178	29748126	0	+	.	ID=NM_206813.;Parent=NM_206813;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_206813.;Parent=NM_206813;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_001170418;Parent=NM_001170418;
Offending exons overlapped:
chr6	hg18_refGene	exon	29746928	29748126	0	+	.	ID=NM_001170418.;Parent=NM_001170418;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_001170418.;Parent=NM_001170418;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_206811;Parent=NM_206811;
Offending exons overlapped:
chr6	hg18_refGene	exon	29747178	29748126	0	+	.	ID=NM_206811.;Parent=NM_206811;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_206811.;Parent=NM_206811;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_206812;Parent=NM_206812;
Offending exons overlapped:
chr6	hg18_refGene	exon	29746928	29748126	0	+	.	ID=NM_206812.;Parent=NM_206812;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_206812.;Parent=NM_206812;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_001170417;Parent=NM_001170417;
Offending exons overlapped:
chr6	hg18_refGene	exon	29746928	29748126	0	+	.	ID=NM_001170417.;Parent=NM_001170417;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_001170417.;Parent=NM_001170417;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29732737	29748126	0	+	.	ID=NM_206809;Parent=NM_206809;
Offending exons overlapped:
chr6	hg18_refGene	exon	29746928	29748126	0	+	.	ID=NM_206809.;Parent=NM_206809;
chr6_cox_hap1	hg18_refGene	exon	1080066	1080382	0	+	.	ID=NM_206809.;Parent=NM_206809;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29748150	29752910	0	-	.	ID=NM_001109809;Parent=NM_001109809;
Offending exons overlapped:
chr6	hg18_refGene	exon	29752637	29752910	0	-	.	ID=NM_001109809.;Parent=NM_001109809;
chr6_cox_hap1	hg18_refGene	exon	1095480	1096844	0	-	.	ID=NM_001109809.;Parent=NM_001109809;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29799096	29802282	0	+	.	ID=NM_001098478;Parent=NM_001098478;
Offending exons overlapped:
chr6	hg18_refGene	exon	29802159	29802282	0	+	.	ID=NM_001098478.;Parent=NM_001098478;
chr6_cox_hap1	hg18_refGene	exon	1143813	1144000	0	+	.	ID=NM_001098478.;Parent=NM_001098478;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29799096	29802282	0	+	.	ID=NM_018950;Parent=NM_018950;
Offending exons overlapped:
chr6	hg18_refGene	exon	29802159	29802282	0	+	.	ID=NM_018950.;Parent=NM_018950;
chr6_cox_hap1	hg18_refGene	exon	1143813	1144000	0	+	.	ID=NM_018950.;Parent=NM_018950;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29799096	29803052	0	+	.	ID=NM_001098479;Parent=NM_001098479;
Offending exons overlapped:
chr6	hg18_refGene	exon	29802639	29803052	0	+	.	ID=NM_001098479.;Parent=NM_001098479;
chr6_cox_hap1	hg18_refGene	exon	1143813	1144000	0	+	.	ID=NM_001098479.;Parent=NM_001098479;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29802357	29824805	0	-	.	ID=NR_026973;Parent=NR_026973;
Offending exons overlapped:
chr6	hg18_refGene	exon	29824656	29824805	0	-	.	ID=NR_026973.;Parent=NR_026973;
chr6_cox_hap1	hg18_refGene	exon	1147070	1147608	0	-	.	ID=NR_026973.;Parent=NR_026973;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29802357	29824805	0	-	.	ID=NR_026972;Parent=NR_026972;
Offending exons overlapped:
chr6	hg18_refGene	exon	29824656	29824805	0	-	.	ID=NR_026972.;Parent=NR_026972;
chr6_cox_hap1	hg18_refGene	exon	1147070	1147608	0	-	.	ID=NR_026972.;Parent=NR_026972;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29826563	29826904	0	-	.	ID=NR_001590;Parent=NR_001590;
Offending exons overlapped:
chr6	hg18_refGene	exon	29826563	29826904	0	-	.	ID=NR_001590.;Parent=NR_001590;
chr6_cox_hap1	hg18_refGene	exon	1171263	1171605	0	-	.	ID=NR_001590.;Parent=NR_001590;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29866788	29868829	0	-	.	ID=NR_002139;Parent=NR_002139;
Offending exons overlapped:
chr6	hg18_refGene	exon	29866788	29868829	0	-	.	ID=NR_002139.;Parent=NR_002139;
chr6_cox_hap1	hg18_refGene	exon	1211428	1213446	0	-	.	ID=NR_002139.;Parent=NR_002139;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29902735	29906878	0	+	.	ID=NM_002127;Parent=NM_002127;
Offending exons overlapped:
chr6	hg18_refGene	exon	29906524	29906878	0	+	.	ID=NM_002127.;Parent=NM_002127;
chr6_cox_hap1	hg18_refGene	exon	1247154	1247219	0	+	.	ID=NM_002127.;Parent=NM_002127;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29947652	29949539	0	-	.	ID=NR_031762;Parent=NR_031762;
Offending exons overlapped:
chr6	hg18_refGene	exon	29947652	29949539	0	-	.	ID=NR_031762.;Parent=NR_031762;
chr6_cox_hap1	hg18_refGene	exon	1295558	1297441	0	-	.	ID=NR_031762.;Parent=NR_031762;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29963362	29966835	0	+	.	ID=NR_001434;Parent=NR_001434;
Offending exons overlapped:
chr6	hg18_refGene	exon	29966195	29966835	0	+	.	ID=NR_001434.;Parent=NR_001434;
chr6_cox_hap1	hg18_refGene	exon	1305632	1305843	0	+	.	ID=NR_001434.;Parent=NR_001434;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	29974787	29978408	0	+	.	ID=NR_001318;Parent=NR_001318;
Offending exons overlapped:
chr6	hg18_refGene	exon	29974787	29978408	0	+	.	ID=NR_001318.;Parent=NR_001318;
chr6_cox_hap1	hg18_refGene	exon	1316948	1320557	0	+	.	ID=NR_001318.;Parent=NR_001318;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30000348	30001407	0	-	.	ID=NR_001317;Parent=NR_001317;
Offending exons overlapped:
chr6	hg18_refGene	exon	30000348	30001407	0	-	.	ID=NR_001317.;Parent=NR_001317;
chr6_cox_hap1	hg18_refGene	exon	1342595	1343658	0	-	.	ID=NR_001317.;Parent=NR_001317;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30018288	30021639	0	+	.	ID=NM_002116;Parent=NM_002116;
Offending exons overlapped:
chr6	hg18_refGene	exon	30021207	30021639	0	+	.	ID=NM_002116.;Parent=NM_002116;
chr6_cox_hap1	hg18_refGene	exon	1358567	1358661	0	+	.	ID=NM_002116.;Parent=NM_002116;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30050871	30054148	0	+	.	ID=NR_028032;Parent=NR_028032;
Offending exons overlapped:
chr6	hg18_refGene	exon	30053974	30054148	0	+	.	ID=NR_028032.;Parent=NR_028032;
chr6_cox_hap1	hg18_refGene	exon	1391102	1391504	0	+	.	ID=NR_028032.;Parent=NR_028032;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30076768	30136940	0	-	.	ID=NR_026751;Parent=NR_026751;
Offending exons overlapped:
chr6	hg18_refGene	exon	30136835	30136940	0	-	.	ID=NR_026751.;Parent=NR_026751;
chr6_cox_hap1	hg18_refGene	exon	1417013	1418733	0	-	.	ID=NR_026751.;Parent=NR_026751;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30081727	30085710	0	+	.	ID=NR_024240;Parent=NR_024240;
Offending exons overlapped:
chr6	hg18_refGene	exon	30085291	30085710	0	+	.	ID=NR_024240.;Parent=NR_024240;
chr6_cox_hap1	hg18_refGene	exon	1421969	1422137	0	+	.	ID=NR_024240.;Parent=NR_024240;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30137015	30140665	0	+	.	ID=NM_170783;Parent=NM_170783;
Offending exons overlapped:
chr6	hg18_refGene	exon	30140429	30140665	0	+	.	ID=NM_170783.;Parent=NM_170783;
chr6_cox_hap1	hg18_refGene	exon	1477649	1478059	0	+	.	ID=NM_170783.;Parent=NM_170783;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30137015	30140665	0	+	.	ID=NM_014596;Parent=NM_014596;
Offending exons overlapped:
chr6	hg18_refGene	exon	30140429	30140665	0	+	.	ID=NM_014596.;Parent=NM_014596;
chr6_cox_hap1	hg18_refGene	exon	1477649	1477788	0	+	.	ID=NM_014596.;Parent=NM_014596;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30142911	30146087	0	+	.	ID=NM_021959;Parent=NM_021959;
Offending exons overlapped:
chr6	hg18_refGene	exon	30144860	30146087	0	+	.	ID=NM_021959.;Parent=NM_021959;
chr6_cox_hap1	hg18_refGene	exon	1483539	1483863	0	+	.	ID=NM_021959.;Parent=NM_021959;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30146023	30151605	0	-	.	ID=NM_170769;Parent=NM_170769;
Offending exons overlapped:
chr6	hg18_refGene	exon	30150979	30151605	0	-	.	ID=NM_170769.;Parent=NM_170769;
chr6_cox_hap1	hg18_refGene	exon	1486651	1487584	0	-	.	ID=NM_170769.;Parent=NM_170769;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30146023	30151607	0	-	.	ID=NM_025236;Parent=NM_025236;
Offending exons overlapped:
chr6	hg18_refGene	exon	30150979	30151607	0	-	.	ID=NM_025236.;Parent=NM_025236;
chr6_cox_hap1	hg18_refGene	exon	1486651	1488075	0	-	.	ID=NM_025236.;Parent=NM_025236;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30178653	30188846	0	-	.	ID=NM_007028;Parent=NM_007028;
Offending exons overlapped:
chr6	hg18_refGene	exon	30188820	30188846	0	-	.	ID=NM_007028.;Parent=NM_007028;
chr6_cox_hap1	hg18_refGene	exon	1519303	1520195	0	-	.	ID=NM_007028.;Parent=NM_007028;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30212489	30224491	0	+	.	ID=NM_138700;Parent=NM_138700;
Offending exons overlapped:
chr6	hg18_refGene	exon	30223481	30224491	0	+	.	ID=NM_138700.;Parent=NM_138700;
chr6_cox_hap1	hg18_refGene	exon	1553151	1553799	0	+	.	ID=NM_138700.;Parent=NM_138700;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30227703	30236690	0	-	.	ID=NM_006778;Parent=NM_006778;
Offending exons overlapped:
chr6	hg18_refGene	exon	30236186	30236690	0	-	.	ID=NM_006778.;Parent=NM_006778;
chr6_cox_hap1	hg18_refGene	exon	1568368	1570907	0	-	.	ID=NM_006778.;Parent=NM_006778;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30227703	30236690	0	-	.	ID=NM_052828;Parent=NM_052828;
Offending exons overlapped:
chr6	hg18_refGene	exon	30236186	30236690	0	-	.	ID=NM_052828.;Parent=NM_052828;
chr6_cox_hap1	hg18_refGene	exon	1568368	1570192	0	-	.	ID=NM_052828.;Parent=NM_052828;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30238962	30248452	0	+	.	ID=NM_033229;Parent=NM_033229;
Offending exons overlapped:
chr6	hg18_refGene	exon	30247588	30248452	0	+	.	ID=NM_033229.;Parent=NM_033229;
chr6_cox_hap1	hg18_refGene	exon	1579617	1580476	0	+	.	ID=NM_033229.;Parent=NM_033229;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30260211	30289132	0	-	.	ID=NM_003449;Parent=NM_003449;
Offending exons overlapped:
chr6	hg18_refGene	exon	30289061	30289132	0	-	.	ID=NM_003449.;Parent=NM_003449;
chr6_cox_hap1	hg18_refGene	exon	1600848	1602951	0	-	.	ID=NM_003449.;Parent=NM_003449;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30335318	30342707	0	+	.	ID=NR_027822;Parent=NR_027822;
Offending exons overlapped:
chr6	hg18_refGene	exon	30339032	30342707	0	+	.	ID=NR_027822.;Parent=NR_027822;
chr6_cox_hap1	hg18_refGene	exon	1675942	1676077	0	+	.	ID=NR_027822.;Parent=NR_027822;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30363153	30402906	0	-	.	ID=NR_024053;Parent=NR_024053;
Offending exons overlapped:
chr6	hg18_refGene	exon	30402110	30402906	0	-	.	ID=NR_024053.;Parent=NR_024053;
chr6_cox_hap1	hg18_refGene	exon	1703704	1708906	0	-	.	ID=NR_024053.;Parent=NR_024053;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30363153	30402906	0	-	.	ID=NR_024052;Parent=NR_024052;
Offending exons overlapped:
chr6	hg18_refGene	exon	30402110	30402906	0	-	.	ID=NR_024052.;Parent=NR_024052;
chr6_cox_hap1	hg18_refGene	exon	1703704	1708906	0	-	.	ID=NR_024052.;Parent=NR_024052;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30402600	30419484	0	+	.	ID=NM_021253;Parent=NM_021253;
Offending exons overlapped:
chr6	hg18_refGene	exon	30417468	30419484	0	+	.	ID=NM_021253.;Parent=NM_021253;
chr6_cox_hap1	hg18_refGene	exon	1743134	1743285	0	+	.	ID=NM_021253.;Parent=NM_021253;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30402987	30419484	0	+	.	ID=NM_172016;Parent=NM_172016;
Offending exons overlapped:
chr6	hg18_refGene	exon	30417468	30419484	0	+	.	ID=NM_172016.;Parent=NM_172016;
chr6_cox_hap1	hg18_refGene	exon	1743521	1743986	0	+	.	ID=NM_172016.;Parent=NM_172016;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30420916	30422611	0	+	.	ID=NM_024839;Parent=NM_024839;
Offending exons overlapped:
chr6	hg18_refGene	exon	30422469	30422611	0	+	.	ID=NM_024839.;Parent=NM_024839;
chr6_cox_hap1	hg18_refGene	exon	1761454	1761522	0	+	.	ID=NM_024839.;Parent=NM_024839;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30565250	30569072	0	+	.	ID=NM_005516;Parent=NM_005516;
Offending exons overlapped:
chr6	hg18_refGene	exon	30568505	30569072	0	+	.	ID=NM_005516.;Parent=NM_005516;
chr6_cox_hap1	hg18_refGene	exon	1905842	1905943	0	+	.	ID=NM_005516.;Parent=NM_005516;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30617136	30633350	0	-	.	ID=NM_005275;Parent=NM_005275;
Offending exons overlapped:
chr6	hg18_refGene	exon	30631887	30633350	0	-	.	ID=NM_005275.;Parent=NM_005275;
chr6_cox_hap1	hg18_refGene	exon	1957712	1962645	0	-	.	ID=NM_005275.;Parent=NM_005275;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30632465	30640452	0	+	.	ID=NM_001077497;Parent=NM_001077497;
Offending exons overlapped:
chr6	hg18_refGene	exon	30638145	30640452	0	+	.	ID=NM_001077497.;Parent=NM_001077497;
chr6_cox_hap1	hg18_refGene	exon	1973042	1973783	0	+	.	ID=NM_001077497.;Parent=NM_001077497;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30632465	30640452	0	+	.	ID=NM_025263;Parent=NM_025263;
Offending exons overlapped:
chr6	hg18_refGene	exon	30638145	30640452	0	+	.	ID=NM_025263.;Parent=NM_025263;
chr6_cox_hap1	hg18_refGene	exon	1973042	1973783	0	+	.	ID=NM_025263.;Parent=NM_025263;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30647149	30667288	0	+	.	ID=NM_001090;Parent=NM_001090;
Offending exons overlapped:
chr6	hg18_refGene	exon	30666291	30667288	0	+	.	ID=NM_001090.;Parent=NM_001090;
chr6_cox_hap1	hg18_refGene	exon	1987728	1987895	0	+	.	ID=NM_001090.;Parent=NM_001090;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30647149	30667288	0	+	.	ID=NM_001025091;Parent=NM_001025091;
Offending exons overlapped:
chr6	hg18_refGene	exon	30666291	30667288	0	+	.	ID=NM_001025091.;Parent=NM_001025091;
chr6_cox_hap1	hg18_refGene	exon	1987728	1987895	0	+	.	ID=NM_001025091.;Parent=NM_001025091;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30660088	30660173	0	+	.	ID=NR_030615;Parent=NR_030615;
Offending exons overlapped:
chr6	hg18_refGene	exon	30660088	30660173	0	+	.	ID=NR_030615.;Parent=NR_030615;
chr6_cox_hap1	hg18_refGene	exon	2000669	2000754	0	+	.	ID=NR_030615.;Parent=NR_030615;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30676161	30692999	0	-	.	ID=NM_002714;Parent=NM_002714;
Offending exons overlapped:
chr6	hg18_refGene	exon	30692980	30692999	0	-	.	ID=NM_002714.;Parent=NM_002714;
chr6_cox_hap1	hg18_refGene	exon	2016742	2017995	0	-	.	ID=NM_002714.;Parent=NM_002714;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30693465	30702153	0	+	.	ID=NM_014046;Parent=NM_014046;
Offending exons overlapped:
chr6	hg18_refGene	exon	30701258	30702153	0	+	.	ID=NM_014046.;Parent=NM_014046;
chr6_cox_hap1	hg18_refGene	exon	2034046	2034280	0	+	.	ID=NM_014046.;Parent=NM_014046;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30702592	30720427	0	+	.	ID=NM_024909;Parent=NM_024909;
Offending exons overlapped:
chr6	hg18_refGene	exon	30719285	30720427	0	+	.	ID=NM_024909.;Parent=NM_024909;
chr6_cox_hap1	hg18_refGene	exon	2043173	2043329	0	+	.	ID=NM_024909.;Parent=NM_024909;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30722795	30728965	0	+	.	ID=NM_001109938;Parent=NM_001109938;
Offending exons overlapped:
chr6	hg18_refGene	exon	30728558	30728965	0	+	.	ID=NM_001109938.;Parent=NM_001109938;
chr6_cox_hap1	hg18_refGene	exon	2063374	2063638	0	+	.	ID=NM_001109938.;Parent=NM_001109938;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30722795	30728965	0	+	.	ID=NM_001161376;Parent=NM_001161376;
Offending exons overlapped:
chr6	hg18_refGene	exon	30728558	30728965	0	+	.	ID=NM_001161376.;Parent=NM_001161376;
chr6_cox_hap1	hg18_refGene	exon	2063374	2064181	0	+	.	ID=NM_001161376.;Parent=NM_001161376;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30722795	30728965	0	+	.	ID=NM_145029;Parent=NM_145029;
Offending exons overlapped:
chr6	hg18_refGene	exon	30728558	30728965	0	+	.	ID=NM_145029.;Parent=NM_145029;
chr6_cox_hap1	hg18_refGene	exon	2063374	2063638	0	+	.	ID=NM_145029.;Parent=NM_145029;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30728876	30748809	0	-	.	ID=NM_003587;Parent=NM_003587;
Offending exons overlapped:
chr6	hg18_refGene	exon	30748391	30748809	0	-	.	ID=NM_003587.;Parent=NM_003587;
chr6_cox_hap1	hg18_refGene	exon	2069447	2069697	0	-	.	ID=NM_003587.;Parent=NM_003587;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30728876	30748809	0	-	.	ID=NM_001164239;Parent=NM_001164239;
Offending exons overlapped:
chr6	hg18_refGene	exon	30748712	30748809	0	-	.	ID=NM_001164239.;Parent=NM_001164239;
chr6_cox_hap1	hg18_refGene	exon	2069447	2069697	0	-	.	ID=NM_001164239.;Parent=NM_001164239;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30752146	30763072	0	-	.	ID=NM_001134870;Parent=NM_001134870;
Offending exons overlapped:
chr6	hg18_refGene	exon	30762870	30763072	0	-	.	ID=NM_001134870.;Parent=NM_001134870;
chr6_cox_hap1	hg18_refGene	exon	2092748	2093645	0	-	.	ID=NM_001134870.;Parent=NM_001134870;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30752146	30763651	0	-	.	ID=NM_133471;Parent=NM_133471;
Offending exons overlapped:
chr6	hg18_refGene	exon	30760164	30763651	0	-	.	ID=NM_133471.;Parent=NM_133471;
chr6_cox_hap1	hg18_refGene	exon	2092748	2093645	0	-	.	ID=NM_133471.;Parent=NM_133471;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30763805	30766748	0	-	.	ID=NM_007243;Parent=NM_007243;
Offending exons overlapped:
chr6	hg18_refGene	exon	30766598	30766748	0	-	.	ID=NM_007243.;Parent=NM_007243;
chr6_cox_hap1	hg18_refGene	exon	2104406	2105299	0	-	.	ID=NM_007243.;Parent=NM_007243;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30775563	30793437	0	-	.	ID=NM_014641;Parent=NM_014641;
Offending exons overlapped:
chr6	hg18_refGene	exon	30793001	30793437	0	-	.	ID=NM_014641.;Parent=NM_014641;
chr6_cox_hap1	hg18_refGene	exon	2116160	2116985	0	-	.	ID=NM_014641.;Parent=NM_014641;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30796136	30801174	0	+	.	ID=NM_178014;Parent=NM_178014;
Offending exons overlapped:
chr6	hg18_refGene	exon	30799096	30801174	0	+	.	ID=NM_178014.;Parent=NM_178014;
chr6_cox_hap1	hg18_refGene	exon	2136732	2136915	0	+	.	ID=NM_178014.;Parent=NM_178014;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30803490	30818432	0	-	.	ID=NM_005803;Parent=NM_005803;
Offending exons overlapped:
chr6	hg18_refGene	exon	30818283	30818432	0	-	.	ID=NM_005803.;Parent=NM_005803;
chr6_cox_hap1	hg18_refGene	exon	2144084	2144495	0	-	.	ID=NM_005803.;Parent=NM_005803;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30818955	30820306	0	-	.	ID=NM_003897;Parent=NM_003897;
Offending exons overlapped:
chr6	hg18_refGene	exon	30820065	30820306	0	-	.	ID=NM_003897.;Parent=NM_003897;
chr6_cox_hap1	hg18_refGene	exon	2159552	2160549	0	-	.	ID=NM_003897.;Parent=NM_003897;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30959840	30975912	0	+	.	ID=NM_001954;Parent=NM_001954;
Offending exons overlapped:
chr6	hg18_refGene	exon	30974912	30975912	0	+	.	ID=NM_001954.;Parent=NM_001954;
chr6_cox_hap1	hg18_refGene	exon	2300466	2300527	0	+	.	ID=NM_001954.;Parent=NM_001954;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30960306	30975912	0	+	.	ID=NM_013993;Parent=NM_013993;
Offending exons overlapped:
chr6	hg18_refGene	exon	30974912	30975912	0	+	.	ID=NM_013993.;Parent=NM_013993;
chr6_cox_hap1	hg18_refGene	exon	2300932	2301092	0	+	.	ID=NM_013993.;Parent=NM_013993;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30964444	30975912	0	+	.	ID=NM_013994;Parent=NM_013994;
Offending exons overlapped:
chr6	hg18_refGene	exon	30974912	30975912	0	+	.	ID=NM_013994.;Parent=NM_013994;
chr6_cox_hap1	hg18_refGene	exon	2305070	2305196	0	+	.	ID=NM_013994.;Parent=NM_013994;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30983956	30989859	0	+	.	ID=NM_001517;Parent=NM_001517;
Offending exons overlapped:
chr6	hg18_refGene	exon	30989567	30989859	0	+	.	ID=NM_001517.;Parent=NM_001517;
chr6_cox_hap1	hg18_refGene	exon	2324559	2324762	0	+	.	ID=NM_001517.;Parent=NM_001517;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30989961	31002212	0	+	.	ID=NM_001167733;Parent=NM_001167733;
Offending exons overlapped:
chr6	hg18_refGene	exon	31001865	31002212	0	+	.	ID=NM_001167733.;Parent=NM_001167733;
chr6_cox_hap1	hg18_refGene	exon	2330564	2330703	0	+	.	ID=NM_001167733.;Parent=NM_001167733;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30989961	31002212	0	+	.	ID=NM_020442;Parent=NM_020442;
Offending exons overlapped:
chr6	hg18_refGene	exon	31001865	31002212	0	+	.	ID=NM_020442.;Parent=NM_020442;
chr6_cox_hap1	hg18_refGene	exon	2330564	2330703	0	+	.	ID=NM_020442.;Parent=NM_020442;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	30990087	31002212	0	+	.	ID=NM_001167734;Parent=NM_001167734;
Offending exons overlapped:
chr6	hg18_refGene	exon	31001865	31002212	0	+	.	ID=NM_001167734.;Parent=NM_001167734;
chr6_cox_hap1	hg18_refGene	exon	2330690	2330828	0	+	.	ID=NM_001167734.;Parent=NM_001167734;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31007106	31007931	0	-	.	ID=NM_205854;Parent=NM_205854;
Offending exons overlapped:
chr6	hg18_refGene	exon	31007792	31007931	0	-	.	ID=NM_205854.;Parent=NM_205854;
chr6_cox_hap1	hg18_refGene	exon	2347557	2347781	0	-	.	ID=NM_205854.;Parent=NM_205854;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31016756	31029977	0	+	.	ID=NM_080870;Parent=NM_080870;
Offending exons overlapped:
chr6	hg18_refGene	exon	31028727	31029977	0	+	.	ID=NM_080870.;Parent=NM_080870;
chr6_cox_hap1	hg18_refGene	exon	2357197	2357278	0	+	.	ID=NM_080870.;Parent=NM_080870;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31059464	31065654	0	+	.	ID=NM_001010909;Parent=NM_001010909;
Offending exons overlapped:
chr6	hg18_refGene	exon	31063756	31065654	0	+	.	ID=NM_001010909.;Parent=NM_001010909;
chr6_cox_hap1	hg18_refGene	exon	2399892	2400203	0	+	.	ID=NM_001010909.;Parent=NM_001010909;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31129963	31135632	0	+	.	ID=NR_003948;Parent=NR_003948;
Offending exons overlapped:
chr6	hg18_refGene	exon	31129963	31135632	0	+	.	ID=NR_003948.;Parent=NR_003948;
chr6_cox_hap1	hg18_refGene	exon	2473197	2478867	0	+	.	ID=NR_003948.;Parent=NR_003948;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31186979	31188311	0	-	.	ID=NM_014070;Parent=NM_014070;
Offending exons overlapped:
chr6	hg18_refGene	exon	31188245	31188311	0	-	.	ID=NM_014070.;Parent=NM_014070;
chr6_cox_hap1	hg18_refGene	exon	2530211	2531279	0	-	.	ID=NM_014070.;Parent=NM_014070;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31190587	31215846	0	+	.	ID=NM_014068;Parent=NM_014068;
Offending exons overlapped:
chr6	hg18_refGene	exon	31215397	31215846	0	+	.	ID=NM_014068.;Parent=NM_014068;
chr6_cox_hap1	hg18_refGene	exon	2533819	2533879	0	+	.	ID=NM_014068.;Parent=NM_014068;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31190849	31196202	0	-	.	ID=NM_001264;Parent=NM_001264;
Offending exons overlapped:
chr6	hg18_refGene	exon	31196091	31196202	0	-	.	ID=NM_001264.;Parent=NM_001264;
chr6_cox_hap1	hg18_refGene	exon	2534081	2536514	0	-	.	ID=NM_001264.;Parent=NM_001264;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31213290	31215106	0	-	.	ID=NM_014069;Parent=NM_014069;
Offending exons overlapped:
chr6	hg18_refGene	exon	31214728	31215106	0	-	.	ID=NM_014069.;Parent=NM_014069;
chr6_cox_hap1	hg18_refGene	exon	2556540	2557312	0	-	.	ID=NM_014069.;Parent=NM_014069;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31218195	31233545	0	-	.	ID=NM_001105564;Parent=NM_001105564;
Offending exons overlapped:
chr6	hg18_refGene	exon	31233141	31233545	0	-	.	ID=NM_001105564.;Parent=NM_001105564;
chr6_cox_hap1	hg18_refGene	exon	2561483	2561760	0	-	.	ID=NM_001105564.;Parent=NM_001105564;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31218195	31233545	0	-	.	ID=NM_001105563;Parent=NM_001105563;
Offending exons overlapped:
chr6	hg18_refGene	exon	31233141	31233545	0	-	.	ID=NM_001105563.;Parent=NM_001105563;
chr6_cox_hap1	hg18_refGene	exon	2561483	2561760	0	-	.	ID=NM_001105563.;Parent=NM_001105563;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31218195	31233994	0	-	.	ID=NM_019052;Parent=NM_019052;
Offending exons overlapped:
chr6	hg18_refGene	exon	31233923	31233994	0	-	.	ID=NM_019052.;Parent=NM_019052;
chr6_cox_hap1	hg18_refGene	exon	2561483	2561760	0	-	.	ID=NM_019052.;Parent=NM_019052;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31234282	31239971	0	+	.	ID=NM_001077511;Parent=NM_001077511;
Offending exons overlapped:
chr6	hg18_refGene	exon	31238233	31239971	0	+	.	ID=NM_001077511.;Parent=NM_001077511;
chr6_cox_hap1	hg18_refGene	exon	2577567	2577763	0	+	.	ID=NM_001077511.;Parent=NM_001077511;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31234282	31239971	0	+	.	ID=NM_007109;Parent=NM_007109;
Offending exons overlapped:
chr6	hg18_refGene	exon	31238233	31239971	0	+	.	ID=NM_007109.;Parent=NM_007109;
chr6_cox_hap1	hg18_refGene	exon	2577567	2577763	0	+	.	ID=NM_007109.;Parent=NM_007109;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31240093	31246430	0	-	.	ID=NM_002701;Parent=NM_002701;
Offending exons overlapped:
chr6	hg18_refGene	exon	31245972	31246430	0	-	.	ID=NM_002701.;Parent=NM_002701;
chr6_cox_hap1	hg18_refGene	exon	2583374	2583904	0	-	.	ID=NM_002701.;Parent=NM_002701;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31240094	31242594	0	-	.	ID=NM_001173531;Parent=NM_001173531;
Offending exons overlapped:
chr6	hg18_refGene	exon	31242290	31242594	0	-	.	ID=NM_001173531.;Parent=NM_001173531;
chr6_cox_hap1	hg18_refGene	exon	2583375	2583904	0	-	.	ID=NM_001173531.;Parent=NM_001173531;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31240094	31242594	0	-	.	ID=NM_203289;Parent=NM_203289;
Offending exons overlapped:
chr6	hg18_refGene	exon	31241683	31242594	0	-	.	ID=NM_203289.;Parent=NM_203289;
chr6_cox_hap1	hg18_refGene	exon	2583375	2583904	0	-	.	ID=NM_203289.;Parent=NM_203289;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31249491	31253655	0	-	.	ID=NR_026816;Parent=NR_026816;
Offending exons overlapped:
chr6	hg18_refGene	exon	31253395	31253655	0	-	.	ID=NR_026816.;Parent=NR_026816;
chr6_cox_hap1	hg18_refGene	exon	2592789	2593087	0	-	.	ID=NR_026816.;Parent=NR_026816;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31273516	31279723	0	+	.	ID=NR_026791;Parent=NR_026791;
Offending exons overlapped:
chr6	hg18_refGene	exon	31278128	31279723	0	+	.	ID=NR_026791.;Parent=NR_026791;
chr6_cox_hap1	hg18_refGene	exon	2616817	2616939	0	+	.	ID=NR_026791.;Parent=NR_026791;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31344508	31347834	0	-	.	ID=NM_002117;Parent=NM_002117;
Offending exons overlapped:
chr6	hg18_refGene	exon	31347755	31347834	0	-	.	ID=NM_002117.;Parent=NM_002117;
chr6_cox_hap1	hg18_refGene	exon	2686291	2686712	0	-	.	ID=NM_002117.;Parent=NM_002117;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31429628	31432968	0	-	.	ID=NM_005514;Parent=NM_005514;
Offending exons overlapped:
chr6	hg18_refGene	exon	31432842	31432968	0	-	.	ID=NM_005514.;Parent=NM_005514;
chr6_cox_hap1	hg18_refGene	exon	2770845	2771269	0	-	.	ID=NM_005514.;Parent=NM_005514;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31479350	31491069	0	+	.	ID=NM_001177519;Parent=NM_001177519;
Offending exons overlapped:
chr6	hg18_refGene	exon	31490768	31491069	0	+	.	ID=NM_001177519.;Parent=NM_001177519;
chr6_cox_hap1	hg18_refGene	exon	2820577	2820685	0	+	.	ID=NM_001177519.;Parent=NM_001177519;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31479350	31491069	0	+	.	ID=NM_000247;Parent=NM_000247;
Offending exons overlapped:
chr6	hg18_refGene	exon	31490768	31491069	0	+	.	ID=NM_000247.;Parent=NM_000247;
chr6_cox_hap1	hg18_refGene	exon	2820577	2820685	0	+	.	ID=NM_000247.;Parent=NM_000247;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31538936	31541563	0	+	.	ID=NM_006674;Parent=NM_006674;
Offending exons overlapped:
chr6	hg18_refGene	exon	31539127	31541563	0	+	.	ID=NM_006674.;Parent=NM_006674;
chr6_cox_hap1	hg18_refGene	exon	2877118	2877217	0	+	.	ID=NM_006674.;Parent=NM_006674;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31546985	31548163	0	+	.	ID=NR_002812;Parent=NR_002812;
Offending exons overlapped:
chr6	hg18_refGene	exon	31546985	31548163	0	+	.	ID=NR_002812.;Parent=NR_002812;
chr6_cox_hap1	hg18_refGene	exon	2885167	2886345	0	+	.	ID=NR_002812.;Parent=NR_002812;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31573834	31586880	0	+	.	ID=NM_005931;Parent=NM_005931;
Offending exons overlapped:
chr6	hg18_refGene	exon	31585538	31586880	0	+	.	ID=NM_005931.;Parent=NM_005931;
chr6_cox_hap1	hg18_refGene	exon	2912031	2912216	0	+	.	ID=NM_005931.;Parent=NM_005931;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31604718	31605987	0	+	.	ID=NM_001011700;Parent=NM_001011700;
Offending exons overlapped:
chr6	hg18_refGene	exon	31605503	31605987	0	+	.	ID=NM_001011700.;Parent=NM_001011700;
chr6_cox_hap1	hg18_refGene	exon	2942908	2943131	0	+	.	ID=NM_001011700.;Parent=NM_001011700;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31605975	31618204	0	-	.	ID=NM_004640;Parent=NM_004640;
Offending exons overlapped:
chr6	hg18_refGene	exon	31617706	31618204	0	-	.	ID=NM_004640.;Parent=NM_004640;
chr6_cox_hap1	hg18_refGene	exon	2944165	2944396	0	-	.	ID=NM_004640.;Parent=NM_004640;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31605975	31618204	0	-	.	ID=NM_080598;Parent=NM_080598;
Offending exons overlapped:
chr6	hg18_refGene	exon	31617706	31618204	0	-	.	ID=NM_080598.;Parent=NM_080598;
chr6_cox_hap1	hg18_refGene	exon	2944165	2944396	0	-	.	ID=NM_080598.;Parent=NM_080598;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31612130	31612205	0	-	.	ID=NR_003140;Parent=NR_003140;
Offending exons overlapped:
chr6	hg18_refGene	exon	31612130	31612205	0	-	.	ID=NR_003140.;Parent=NR_003140;
chr6_cox_hap1	hg18_refGene	exon	2950320	2950395	0	-	.	ID=NR_003140.;Parent=NR_003140;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31616857	31616934	0	-	.	ID=NR_003065;Parent=NR_003065;
Offending exons overlapped:
chr6	hg18_refGene	exon	31616857	31616934	0	-	.	ID=NR_003065.;Parent=NR_003065;
chr6_cox_hap1	hg18_refGene	exon	2955044	2955121	0	-	.	ID=NR_003065.;Parent=NR_003065;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31620219	31622606	0	-	.	ID=NM_138282;Parent=NM_138282;
Offending exons overlapped:
chr6	hg18_refGene	exon	31622388	31622606	0	-	.	ID=NM_138282.;Parent=NM_138282;
chr6_cox_hap1	hg18_refGene	exon	2958406	2959524	0	-	.	ID=NM_138282.;Parent=NM_138282;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31620219	31622606	0	-	.	ID=NM_130463;Parent=NM_130463;
Offending exons overlapped:
chr6	hg18_refGene	exon	31622234	31622606	0	-	.	ID=NM_130463.;Parent=NM_130463;
chr6_cox_hap1	hg18_refGene	exon	2958406	2959524	0	-	.	ID=NM_130463.;Parent=NM_130463;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31622607	31634584	0	+	.	ID=NM_001144963;Parent=NM_001144963;
Offending exons overlapped:
chr6	hg18_refGene	exon	31633778	31634584	0	+	.	ID=NM_001144963.;Parent=NM_001144963;
chr6_cox_hap1	hg18_refGene	exon	2960790	2960912	0	+	.	ID=NM_001144963.;Parent=NM_001144963;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31622607	31634584	0	+	.	ID=NM_001144962;Parent=NM_001144962;
Offending exons overlapped:
chr6	hg18_refGene	exon	31633778	31634584	0	+	.	ID=NM_001144962.;Parent=NM_001144962;
chr6_cox_hap1	hg18_refGene	exon	2960790	2960912	0	+	.	ID=NM_001144962.;Parent=NM_001144962;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31623332	31634584	0	+	.	ID=NM_001144961;Parent=NM_001144961;
Offending exons overlapped:
chr6	hg18_refGene	exon	31633778	31634584	0	+	.	ID=NM_001144961.;Parent=NM_001144961;
chr6_cox_hap1	hg18_refGene	exon	2961514	2961689	0	+	.	ID=NM_001144961.;Parent=NM_001144961;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31623332	31634584	0	+	.	ID=NM_005007;Parent=NM_005007;
Offending exons overlapped:
chr6	hg18_refGene	exon	31633778	31634584	0	+	.	ID=NM_005007.;Parent=NM_005007;
chr6_cox_hap1	hg18_refGene	exon	2961514	2961689	0	+	.	ID=NM_005007.;Parent=NM_005007;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31647855	31650077	0	+	.	ID=NM_001159740;Parent=NM_001159740;
Offending exons overlapped:
chr6	hg18_refGene	exon	31649037	31650077	0	+	.	ID=NM_001159740.;Parent=NM_001159740;
chr6_cox_hap1	hg18_refGene	exon	2985999	2986202	0	+	.	ID=NM_001159740.;Parent=NM_001159740;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31648072	31650077	0	+	.	ID=NM_000595;Parent=NM_000595;
Offending exons overlapped:
chr6	hg18_refGene	exon	31649037	31650077	0	+	.	ID=NM_000595.;Parent=NM_000595;
chr6_cox_hap1	hg18_refGene	exon	2986216	2986346	0	+	.	ID=NM_000595.;Parent=NM_000595;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31651329	31654091	0	+	.	ID=NM_000594;Parent=NM_000594;
Offending exons overlapped:
chr6	hg18_refGene	exon	31652872	31654091	0	+	.	ID=NM_000594.;Parent=NM_000594;
chr6_cox_hap1	hg18_refGene	exon	2989473	2989827	0	+	.	ID=NM_000594.;Parent=NM_000594;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31656315	31658181	0	-	.	ID=NM_002341;Parent=NM_002341;
Offending exons overlapped:
chr6	hg18_refGene	exon	31658012	31658181	0	-	.	ID=NM_002341.;Parent=NM_002341;
chr6_cox_hap1	hg18_refGene	exon	2994459	2995063	0	-	.	ID=NM_002341.;Parent=NM_002341;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31656315	31658181	0	-	.	ID=NM_009588;Parent=NM_009588;
Offending exons overlapped:
chr6	hg18_refGene	exon	31658012	31658181	0	-	.	ID=NM_009588.;Parent=NM_009588;
chr6_cox_hap1	hg18_refGene	exon	2994459	2995063	0	-	.	ID=NM_009588.;Parent=NM_009588;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31661935	31664664	0	+	.	ID=NR_029462;Parent=NR_029462;
Offending exons overlapped:
chr6	hg18_refGene	exon	31664319	31664664	0	+	.	ID=NR_029462.;Parent=NR_029462;
chr6_cox_hap1	hg18_refGene	exon	3000079	3000215	0	+	.	ID=NR_029462.;Parent=NR_029462;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31661935	31664664	0	+	.	ID=NM_205838;Parent=NM_205838;
Offending exons overlapped:
chr6	hg18_refGene	exon	31664274	31664664	0	+	.	ID=NM_205838.;Parent=NM_205838;
chr6_cox_hap1	hg18_refGene	exon	3000079	3000215	0	+	.	ID=NM_205838.;Parent=NM_205838;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31661935	31664664	0	+	.	ID=NR_029461;Parent=NR_029461;
Offending exons overlapped:
chr6	hg18_refGene	exon	31664274	31664664	0	+	.	ID=NR_029461.;Parent=NR_029461;
chr6_cox_hap1	hg18_refGene	exon	3000079	3000215	0	+	.	ID=NR_029461.;Parent=NR_029461;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31661935	31664664	0	+	.	ID=NM_205839;Parent=NM_205839;
Offending exons overlapped:
chr6	hg18_refGene	exon	31664274	31664664	0	+	.	ID=NM_205839.;Parent=NM_205839;
chr6_cox_hap1	hg18_refGene	exon	3000079	3000215	0	+	.	ID=NM_205839.;Parent=NM_205839;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31662455	31664664	0	+	.	ID=NM_205837;Parent=NM_205837;
Offending exons overlapped:
chr6	hg18_refGene	exon	31664253	31664664	0	+	.	ID=NM_205837.;Parent=NM_205837;
chr6_cox_hap1	hg18_refGene	exon	3000599	3000707	0	+	.	ID=NM_205837.;Parent=NM_205837;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31662956	31664664	0	+	.	ID=NM_001166538;Parent=NM_001166538;
Offending exons overlapped:
chr6	hg18_refGene	exon	31664253	31664664	0	+	.	ID=NM_001166538.;Parent=NM_001166538;
chr6_cox_hap1	hg18_refGene	exon	3001100	3001218	0	+	.	ID=NM_001166538.;Parent=NM_001166538;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31662956	31664664	0	+	.	ID=NM_205840;Parent=NM_205840;
Offending exons overlapped:
chr6	hg18_refGene	exon	31664274	31664664	0	+	.	ID=NM_205840.;Parent=NM_205840;
chr6_cox_hap1	hg18_refGene	exon	3001100	3001218	0	+	.	ID=NM_205840.;Parent=NM_205840;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31662956	31664664	0	+	.	ID=NM_007161;Parent=NM_007161;
Offending exons overlapped:
chr6	hg18_refGene	exon	31664253	31664664	0	+	.	ID=NM_007161.;Parent=NM_007161;
chr6_cox_hap1	hg18_refGene	exon	3001100	3001218	0	+	.	ID=NM_007161.;Parent=NM_007161;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31664639	31668741	0	-	.	ID=NM_147130;Parent=NM_147130;
Offending exons overlapped:
chr6	hg18_refGene	exon	31668435	31668741	0	-	.	ID=NM_147130.;Parent=NM_147130;
chr6_cox_hap1	hg18_refGene	exon	3002779	3003072	0	-	.	ID=NM_147130.;Parent=NM_147130;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31664639	31668741	0	-	.	ID=NM_001145466;Parent=NM_001145466;
Offending exons overlapped:
chr6	hg18_refGene	exon	31668435	31668741	0	-	.	ID=NM_001145466.;Parent=NM_001145466;
chr6_cox_hap1	hg18_refGene	exon	3002779	3003127	0	-	.	ID=NM_001145466.;Parent=NM_001145466;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31665030	31668741	0	-	.	ID=NM_001145467;Parent=NM_001145467;
Offending exons overlapped:
chr6	hg18_refGene	exon	31668435	31668741	0	-	.	ID=NM_001145467.;Parent=NM_001145467;
chr6_cox_hap1	hg18_refGene	exon	3003170	3003284	0	-	.	ID=NM_001145467.;Parent=NM_001145467;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31690973	31692775	0	+	.	ID=NM_004847;Parent=NM_004847;
Offending exons overlapped:
chr6	hg18_refGene	exon	31691426	31692775	0	+	.	ID=NM_004847.;Parent=NM_004847;
chr6_cox_hap1	hg18_refGene	exon	3029119	3029195	0	+	.	ID=NM_004847.;Parent=NM_004847;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31691012	31692777	0	+	.	ID=NM_001623;Parent=NM_001623;
Offending exons overlapped:
chr6	hg18_refGene	exon	31692572	31692777	0	+	.	ID=NM_001623.;Parent=NM_001623;
chr6_cox_hap1	hg18_refGene	exon	3029158	3029256	0	+	.	ID=NM_001623.;Parent=NM_001623;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31691768	31692777	0	+	.	ID=NM_032955;Parent=NM_032955;
Offending exons overlapped:
chr6	hg18_refGene	exon	31692572	31692777	0	+	.	ID=NM_032955.;Parent=NM_032955;
chr6_cox_hap1	hg18_refGene	exon	3029914	3030047	0	+	.	ID=NM_032955.;Parent=NM_032955;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31696429	31713533	0	+	.	ID=NM_080686;Parent=NM_080686;
Offending exons overlapped:
chr6	hg18_refGene	exon	31713202	31713533	0	+	.	ID=NM_080686.;Parent=NM_080686;
chr6_cox_hap1	hg18_refGene	exon	3034574	3034759	0	+	.	ID=NM_080686.;Parent=NM_080686;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31698835	31698966	0	+	.	ID=NR_002971;Parent=NR_002971;
Offending exons overlapped:
chr6	hg18_refGene	exon	31698835	31698966	0	+	.	ID=NR_002971.;Parent=NR_002971;
chr6_cox_hap1	hg18_refGene	exon	3036977	3037108	0	+	.	ID=NR_002971.;Parent=NR_002971;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31714784	31728149	0	-	.	ID=NM_001098534;Parent=NM_001098534;
Offending exons overlapped:
chr6	hg18_refGene	exon	31728003	31728149	0	-	.	ID=NM_001098534.;Parent=NM_001098534;
chr6_cox_hap1	hg18_refGene	exon	3052923	3053125	0	-	.	ID=NM_001098534.;Parent=NM_001098534;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31714784	31728456	0	-	.	ID=NM_080702;Parent=NM_080702;
Offending exons overlapped:
chr6	hg18_refGene	exon	31728180	31728456	0	-	.	ID=NM_080702.;Parent=NM_080702;
chr6_cox_hap1	hg18_refGene	exon	3052923	3053125	0	-	.	ID=NM_080702.;Parent=NM_080702;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31714784	31728456	0	-	.	ID=NM_080703;Parent=NM_080703;
Offending exons overlapped:
chr6	hg18_refGene	exon	31728156	31728456	0	-	.	ID=NM_080703.;Parent=NM_080703;
chr6_cox_hap1	hg18_refGene	exon	3052923	3053125	0	-	.	ID=NM_080703.;Parent=NM_080703;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31714784	31728456	0	-	.	ID=NM_004639;Parent=NM_004639;
Offending exons overlapped:
chr6	hg18_refGene	exon	31728156	31728456	0	-	.	ID=NM_004639.;Parent=NM_004639;
chr6_cox_hap1	hg18_refGene	exon	3052923	3053125	0	-	.	ID=NM_004639.;Parent=NM_004639;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31731650	31733966	0	+	.	ID=NM_019101;Parent=NM_019101;
Offending exons overlapped:
chr6	hg18_refGene	exon	31733820	31733966	0	+	.	ID=NM_019101.;Parent=NM_019101;
chr6_cox_hap1	hg18_refGene	exon	3069796	3069982	0	+	.	ID=NM_019101.;Parent=NM_019101;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31734054	31736528	0	-	.	ID=NM_021184;Parent=NM_021184;
Offending exons overlapped:
chr6	hg18_refGene	exon	31734054	31736528	0	-	.	ID=NM_021184.;Parent=NM_021184;
chr6_cox_hap1	hg18_refGene	exon	3072200	3074675	0	-	.	ID=NM_021184.;Parent=NM_021184;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31737841	31741142	0	-	.	ID=NM_033177;Parent=NM_033177;
Offending exons overlapped:
chr6	hg18_refGene	exon	31740597	31741142	0	-	.	ID=NM_033177.;Parent=NM_033177;
chr6_cox_hap1	hg18_refGene	exon	3075988	3076613	0	-	.	ID=NM_033177.;Parent=NM_033177;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31741636	31745822	0	+	.	ID=NM_001320;Parent=NM_001320;
Offending exons overlapped:
chr6	hg18_refGene	exon	31745592	31745822	0	+	.	ID=NM_001320.;Parent=NM_001320;
chr6_cox_hap1	hg18_refGene	exon	3079784	3080112	0	+	.	ID=NM_001320.;Parent=NM_001320;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31746707	31748206	0	+	.	ID=NM_021221;Parent=NM_021221;
Offending exons overlapped:
chr6	hg18_refGene	exon	31747620	31748206	0	+	.	ID=NM_021221.;Parent=NM_021221;
chr6_cox_hap1	hg18_refGene	exon	3084855	3084912	0	+	.	ID=NM_021221.;Parent=NM_021221;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31752440	31756129	0	-	.	ID=NM_025262;Parent=NM_025262;
Offending exons overlapped:
chr6	hg18_refGene	exon	31756009	31756129	0	-	.	ID=NM_025262.;Parent=NM_025262;
chr6_cox_hap1	hg18_refGene	exon	3090588	3091024	0	-	.	ID=NM_025262.;Parent=NM_025262;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31762705	31778829	0	-	.	ID=NR_033488;Parent=NR_033488;
Offending exons overlapped:
chr6	hg18_refGene	exon	31778368	31778829	0	-	.	ID=NR_033488.;Parent=NR_033488;
chr6_cox_hap1	hg18_refGene	exon	3100854	3101198	0	-	.	ID=NR_033488.;Parent=NR_033488;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31762705	31778829	0	-	.	ID=NM_001177515;Parent=NM_001177515;
Offending exons overlapped:
chr6	hg18_refGene	exon	31778368	31778829	0	-	.	ID=NM_001177515.;Parent=NM_001177515;
chr6_cox_hap1	hg18_refGene	exon	3100854	3101198	0	-	.	ID=NM_001177515.;Parent=NM_001177515;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31762705	31779116	0	-	.	ID=NM_021160;Parent=NM_021160;
Offending exons overlapped:
chr6	hg18_refGene	exon	31778906	31779116	0	-	.	ID=NM_021160.;Parent=NM_021160;
chr6_cox_hap1	hg18_refGene	exon	3100854	3101198	0	-	.	ID=NM_021160.;Parent=NM_021160;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31762705	31779116	0	-	.	ID=NR_033489;Parent=NR_033489;
Offending exons overlapped:
chr6	hg18_refGene	exon	31778906	31779116	0	-	.	ID=NR_033489.;Parent=NR_033489;
chr6_cox_hap1	hg18_refGene	exon	3100854	3101198	0	-	.	ID=NR_033489.;Parent=NR_033489;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31782663	31786351	0	+	.	ID=NM_001003693;Parent=NM_001003693;
Offending exons overlapped:
chr6	hg18_refGene	exon	31786323	31786351	0	+	.	ID=NM_001003693.;Parent=NM_001003693;
chr6_cox_hap1	hg18_refGene	exon	3120810	3120861	0	+	.	ID=NM_001003693.;Parent=NM_001003693;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31787732	31789821	0	-	.	ID=NR_024541;Parent=NR_024541;
Offending exons overlapped:
chr6	hg18_refGene	exon	31789517	31789821	0	-	.	ID=NR_024541.;Parent=NR_024541;
chr6_cox_hap1	hg18_refGene	exon	3125873	3126012	0	-	.	ID=NR_024541.;Parent=NR_024541;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31788097	31789821	0	-	.	ID=NR_003673;Parent=NR_003673;
Offending exons overlapped:
chr6	hg18_refGene	exon	31789517	31789821	0	-	.	ID=NR_003673.;Parent=NR_003673;
chr6_cox_hap1	hg18_refGene	exon	3126238	3126458	0	-	.	ID=NR_003673.;Parent=NR_003673;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31791112	31793560	0	+	.	ID=NM_021246;Parent=NM_021246;
Offending exons overlapped:
chr6	hg18_refGene	exon	31793337	31793560	0	+	.	ID=NM_021246.;Parent=NM_021246;
chr6_cox_hap1	hg18_refGene	exon	3129253	3129307	0	+	.	ID=NM_021246.;Parent=NM_021246;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31794404	31797489	0	-	.	ID=NM_025261;Parent=NM_025261;
Offending exons overlapped:
chr6	hg18_refGene	exon	31797384	31797489	0	-	.	ID=NM_025261.;Parent=NM_025261;
chr6_cox_hap1	hg18_refGene	exon	3132549	3133211	0	-	.	ID=NM_025261.;Parent=NM_025261;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31799140	31800830	0	+	.	ID=NM_138273;Parent=NM_138273;
Offending exons overlapped:
chr6	hg18_refGene	exon	31800726	31800830	0	+	.	ID=NM_138273.;Parent=NM_138273;
chr6_cox_hap1	hg18_refGene	exon	3137285	3137345	0	+	.	ID=NM_138273.;Parent=NM_138273;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31799140	31800830	0	+	.	ID=NM_025260;Parent=NM_025260;
Offending exons overlapped:
chr6	hg18_refGene	exon	31800726	31800830	0	+	.	ID=NM_025260.;Parent=NM_025260;
chr6_cox_hap1	hg18_refGene	exon	3137285	3137345	0	+	.	ID=NM_025260.;Parent=NM_025260;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31799140	31800830	0	+	.	ID=NM_138274;Parent=NM_138274;
Offending exons overlapped:
chr6	hg18_refGene	exon	31800726	31800830	0	+	.	ID=NM_138274.;Parent=NM_138274;
chr6_cox_hap1	hg18_refGene	exon	3137285	3137345	0	+	.	ID=NM_138274.;Parent=NM_138274;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31799140	31800830	0	+	.	ID=NM_138272;Parent=NM_138272;
Offending exons overlapped:
chr6	hg18_refGene	exon	31800726	31800830	0	+	.	ID=NM_138272.;Parent=NM_138272;
chr6_cox_hap1	hg18_refGene	exon	3137285	3137345	0	+	.	ID=NM_138272.;Parent=NM_138272;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31799140	31800830	0	+	.	ID=NM_138275;Parent=NM_138275;
Offending exons overlapped:
chr6	hg18_refGene	exon	31800726	31800830	0	+	.	ID=NM_138275.;Parent=NM_138275;
chr6_cox_hap1	hg18_refGene	exon	3137285	3137345	0	+	.	ID=NM_138275.;Parent=NM_138275;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31799140	31800830	0	+	.	ID=NM_138277;Parent=NM_138277;
Offending exons overlapped:
chr6	hg18_refGene	exon	31800502	31800830	0	+	.	ID=NM_138277.;Parent=NM_138277;
chr6_cox_hap1	hg18_refGene	exon	3137285	3137345	0	+	.	ID=NM_138277.;Parent=NM_138277;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31802796	31806018	0	-	.	ID=NM_013974;Parent=NM_013974;
Offending exons overlapped:
chr6	hg18_refGene	exon	31805807	31806018	0	-	.	ID=NM_013974.;Parent=NM_013974;
chr6_cox_hap1	hg18_refGene	exon	3140941	3141254	0	-	.	ID=NM_013974.;Parent=NM_013974;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31806337	31812320	0	-	.	ID=NM_001288;Parent=NM_001288;
Offending exons overlapped:
chr6	hg18_refGene	exon	31812018	31812320	0	-	.	ID=NM_001288.;Parent=NM_001288;
chr6_cox_hap1	hg18_refGene	exon	3144482	3144904	0	-	.	ID=NM_001288.;Parent=NM_001288;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31815704	31838429	0	+	.	ID=NM_172166;Parent=NM_172166;
Offending exons overlapped:
chr6	hg18_refGene	exon	31838176	31838429	0	+	.	ID=NM_172166.;Parent=NM_172166;
chr6_cox_hap1	hg18_refGene	exon	3153841	3153955	0	+	.	ID=NM_172166.;Parent=NM_172166;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31815704	31838429	0	+	.	ID=NM_172165;Parent=NM_172165;
Offending exons overlapped:
chr6	hg18_refGene	exon	31838176	31838429	0	+	.	ID=NM_172165.;Parent=NM_172165;
chr6_cox_hap1	hg18_refGene	exon	3153841	3153955	0	+	.	ID=NM_172165.;Parent=NM_172165;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31815704	31838429	0	+	.	ID=NM_025259;Parent=NM_025259;
Offending exons overlapped:
chr6	hg18_refGene	exon	31838176	31838429	0	+	.	ID=NM_025259.;Parent=NM_025259;
chr6_cox_hap1	hg18_refGene	exon	3153841	3153955	0	+	.	ID=NM_025259.;Parent=NM_025259;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31815704	31838429	0	+	.	ID=NM_002441;Parent=NM_002441;
Offending exons overlapped:
chr6	hg18_refGene	exon	31838176	31838429	0	+	.	ID=NM_002441.;Parent=NM_002441;
chr6_cox_hap1	hg18_refGene	exon	3153841	3154113	0	+	.	ID=NM_002441.;Parent=NM_002441;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31838752	31840603	0	+	.	ID=NM_001039651;Parent=NM_001039651;
Offending exons overlapped:
chr6	hg18_refGene	exon	31840192	31840603	0	+	.	ID=NM_001039651.;Parent=NM_001039651;
chr6_cox_hap1	hg18_refGene	exon	3176866	3177038	0	+	.	ID=NM_001039651.;Parent=NM_001039651;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31841350	31853087	0	-	.	ID=NM_025258;Parent=NM_025258;
Offending exons overlapped:
chr6	hg18_refGene	exon	31852865	31853087	0	-	.	ID=NM_025258.;Parent=NM_025258;
chr6_cox_hap1	hg18_refGene	exon	3179465	3179641	0	-	.	ID=NM_025258.;Parent=NM_025258;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31853276	31871691	0	-	.	ID=NM_006295;Parent=NM_006295;
Offending exons overlapped:
chr6	hg18_refGene	exon	31871302	31871691	0	-	.	ID=NM_006295.;Parent=NM_006295;
chr6_cox_hap1	hg18_refGene	exon	3191375	3191517	0	-	.	ID=NM_006295.;Parent=NM_006295;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31873153	31882722	0	-	.	ID=NM_021177;Parent=NM_021177;
Offending exons overlapped:
chr6	hg18_refGene	exon	31882511	31882722	0	-	.	ID=NM_021177.;Parent=NM_021177;
chr6_cox_hap1	hg18_refGene	exon	3211249	3211734	0	-	.	ID=NM_021177.;Parent=NM_021177;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31885375	31890814	0	-	.	ID=NM_005527;Parent=NM_005527;
Offending exons overlapped:
chr6	hg18_refGene	exon	31890645	31890814	0	-	.	ID=NM_005527.;Parent=NM_005527;
chr6_cox_hap1	hg18_refGene	exon	3223484	3225850	0	-	.	ID=NM_005527.;Parent=NM_005527;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31891270	31893698	0	+	.	ID=NM_005345;Parent=NM_005345;
Offending exons overlapped:
chr6	hg18_refGene	exon	31891270	31893698	0	+	.	ID=NM_005345.;Parent=NM_005345;
chr6_cox_hap1	hg18_refGene	exon	3229378	3231806	0	+	.	ID=NM_005345.;Parent=NM_005345;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31903491	31906010	0	+	.	ID=NM_005346;Parent=NM_005346;
Offending exons overlapped:
chr6	hg18_refGene	exon	31903491	31906010	0	+	.	ID=NM_005346.;Parent=NM_005346;
chr6_cox_hap1	hg18_refGene	exon	3241601	3244123	0	+	.	ID=NM_005346.;Parent=NM_005346;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31910672	31915520	0	+	.	ID=NM_001040438;Parent=NM_001040438;
Offending exons overlapped:
chr6	hg18_refGene	exon	31915299	31915520	0	+	.	ID=NM_001040438.;Parent=NM_001040438;
chr6_cox_hap1	hg18_refGene	exon	3248776	3249060	0	+	.	ID=NM_001040438.;Parent=NM_001040438;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31910672	31915520	0	+	.	ID=NM_001040437;Parent=NM_001040437;
Offending exons overlapped:
chr6	hg18_refGene	exon	31915299	31915520	0	+	.	ID=NM_001040437.;Parent=NM_001040437;
chr6_cox_hap1	hg18_refGene	exon	3248776	3249060	0	+	.	ID=NM_001040437.;Parent=NM_001040437;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31911019	31911082	0	+	.	ID=NR_002745;Parent=NR_002745;
Offending exons overlapped:
chr6	hg18_refGene	exon	31911019	31911082	0	+	.	ID=NR_002745.;Parent=NR_002745;
chr6_cox_hap1	hg18_refGene	exon	3249123	3249185	0	+	.	ID=NR_002745.;Parent=NR_002745;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31912832	31912894	0	+	.	ID=NR_002742;Parent=NR_002742;
Offending exons overlapped:
chr6	hg18_refGene	exon	31912832	31912894	0	+	.	ID=NR_002742.;Parent=NR_002742;
chr6_cox_hap1	hg18_refGene	exon	3250934	3250996	0	+	.	ID=NR_002742.;Parent=NR_002742;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31934808	31938688	0	-	.	ID=NM_000434;Parent=NM_000434;
Offending exons overlapped:
chr6	hg18_refGene	exon	31938374	31938688	0	-	.	ID=NM_000434.;Parent=NM_000434;
chr6_cox_hap1	hg18_refGene	exon	3273083	3273976	0	-	.	ID=NM_000434.;Parent=NM_000434;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31938949	31954802	0	-	.	ID=NM_025257;Parent=NM_025257;
Offending exons overlapped:
chr6	hg18_refGene	exon	31954697	31954802	0	-	.	ID=NM_025257.;Parent=NM_025257;
chr6_cox_hap1	hg18_refGene	exon	3277224	3277779	0	-	.	ID=NM_025257.;Parent=NM_025257;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31938951	31953427	0	-	.	ID=NM_001178045;Parent=NM_001178045;
Offending exons overlapped:
chr6	hg18_refGene	exon	31953319	31953427	0	-	.	ID=NM_001178045.;Parent=NM_001178045;
chr6_cox_hap1	hg18_refGene	exon	3277226	3277779	0	-	.	ID=NM_001178045.;Parent=NM_001178045;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31938951	31954802	0	-	.	ID=NM_001178044;Parent=NM_001178044;
Offending exons overlapped:
chr6	hg18_refGene	exon	31954697	31954802	0	-	.	ID=NM_001178044.;Parent=NM_001178044;
chr6_cox_hap1	hg18_refGene	exon	3277226	3277779	0	-	.	ID=NM_001178044.;Parent=NM_001178044;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31955516	31973443	0	-	.	ID=NM_025256;Parent=NM_025256;
Offending exons overlapped:
chr6	hg18_refGene	exon	31973392	31973443	0	-	.	ID=NM_025256.;Parent=NM_025256;
chr6_cox_hap1	hg18_refGene	exon	3293797	3294302	0	-	.	ID=NM_025256.;Parent=NM_025256;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31955516	31973443	0	-	.	ID=NM_006709;Parent=NM_006709;
Offending exons overlapped:
chr6	hg18_refGene	exon	31973392	31973443	0	-	.	ID=NM_006709.;Parent=NM_006709;
chr6_cox_hap1	hg18_refGene	exon	3293797	3294302	0	-	.	ID=NM_006709.;Parent=NM_006709;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31975373	31977748	0	-	.	ID=NM_181842;Parent=NM_181842;
Offending exons overlapped:
chr6	hg18_refGene	exon	31977593	31977748	0	-	.	ID=NM_181842.;Parent=NM_181842;
chr6_cox_hap1	hg18_refGene	exon	3313655	3315363	0	-	.	ID=NM_181842.;Parent=NM_181842;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	31976755	32021427	0	+	.	ID=NM_001178063;Parent=NM_001178063;
Offending exons overlapped:
chr6	hg18_refGene	exon	32020934	32021427	0	+	.	ID=NM_001178063.;Parent=NM_001178063;
chr6_cox_hap1	hg18_refGene	exon	3315037	3315177	0	+	.	ID=NM_001178063.;Parent=NM_001178063;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32003245	32021427	0	+	.	ID=NM_001145903;Parent=NM_001145903;
Offending exons overlapped:
chr6	hg18_refGene	exon	32020934	32021427	0	+	.	ID=NM_001145903.;Parent=NM_001145903;
chr6_cox_hap1	hg18_refGene	exon	3341529	3341838	0	+	.	ID=NM_001145903.;Parent=NM_001145903;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32003245	32021427	0	+	.	ID=NM_000063;Parent=NM_000063;
Offending exons overlapped:
chr6	hg18_refGene	exon	32020934	32021427	0	+	.	ID=NM_000063.;Parent=NM_000063;
chr6_cox_hap1	hg18_refGene	exon	3341529	3341838	0	+	.	ID=NM_000063.;Parent=NM_000063;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32021700	32027840	0	+	.	ID=NM_001710;Parent=NM_001710;
Offending exons overlapped:
chr6	hg18_refGene	exon	32027631	32027840	0	+	.	ID=NM_001710.;Parent=NM_001710;
chr6_cox_hap1	hg18_refGene	exon	3359984	3360325	0	+	.	ID=NM_001710.;Parent=NM_001710;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32027843	32034843	0	-	.	ID=NM_002904;Parent=NM_002904;
Offending exons overlapped:
chr6	hg18_refGene	exon	32034648	32034843	0	-	.	ID=NM_002904.;Parent=NM_002904;
chr6_cox_hap1	hg18_refGene	exon	3366127	3366438	0	-	.	ID=NM_002904.;Parent=NM_002904;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32032595	32032696	0	-	.	ID=NR_031601;Parent=NR_031601;
Offending exons overlapped:
chr6	hg18_refGene	exon	32032595	32032696	0	-	.	ID=NR_031601.;Parent=NR_031601;
chr6_cox_hap1	hg18_refGene	exon	3370879	3370980	0	-	.	ID=NR_031601.;Parent=NR_031601;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32034560	32045511	0	+	.	ID=NM_006929;Parent=NM_006929;
Offending exons overlapped:
chr6	hg18_refGene	exon	32045271	32045511	0	+	.	ID=NM_006929.;Parent=NM_006929;
chr6_cox_hap1	hg18_refGene	exon	3372844	3373254	0	+	.	ID=NM_006929.;Parent=NM_006929;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32045567	32048011	0	-	.	ID=NM_005510;Parent=NM_005510;
Offending exons overlapped:
chr6	hg18_refGene	exon	32047685	32048011	0	-	.	ID=NM_005510.;Parent=NM_005510;
chr6_cox_hap1	hg18_refGene	exon	3383851	3384064	0	-	.	ID=NM_005510.;Parent=NM_005510;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32046931	32057201	0	+	.	ID=NR_026717;Parent=NR_026717;
Offending exons overlapped:
chr6	hg18_refGene	exon	32056760	32057201	0	+	.	ID=NR_026717.;Parent=NR_026717;
chr6_cox_hap1	hg18_refGene	exon	3385215	3385314	0	+	.	ID=NR_026717.;Parent=NR_026717;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32047625	32057202	0	+	.	ID=NM_004197;Parent=NM_004197;
Offending exons overlapped:
chr6	hg18_refGene	exon	32056760	32057202	0	+	.	ID=NM_004197.;Parent=NM_004197;
chr6_cox_hap1	hg18_refGene	exon	3385909	3386256	0	+	.	ID=NM_004197.;Parent=NM_004197;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32047625	32057202	0	+	.	ID=NM_032454;Parent=NM_032454;
Offending exons overlapped:
chr6	hg18_refGene	exon	32056760	32057202	0	+	.	ID=NM_032454.;Parent=NM_032454;
chr6_cox_hap1	hg18_refGene	exon	3385909	3386256	0	+	.	ID=NM_032454.;Parent=NM_032454;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32057813	32078435	0	+	.	ID=NM_007293;Parent=NM_007293;
Offending exons overlapped:
chr6	hg18_refGene	exon	32078154	32078435	0	+	.	ID=NM_007293.;Parent=NM_007293;
chr6_cox_hap1	hg18_refGene	exon	3396097	3396212	0	+	.	ID=NM_007293.;Parent=NM_007293;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32057813	32078436	0	+	.	ID=NM_001002029;Parent=NM_001002029;
Offending exons overlapped:
chr6	hg18_refGene	exon	32078154	32078436	0	+	.	ID=NM_001002029.;Parent=NM_001002029;
chr6_cox_hap1	hg18_refGene	exon	3396097	3396212	0	+	.	ID=NM_001002029.;Parent=NM_001002029;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32114061	32117398	0	+	.	ID=NM_000500;Parent=NM_000500;
Offending exons overlapped:
chr6	hg18_refGene	exon	32116625	32117398	0	+	.	ID=NM_000500.;Parent=NM_000500;
chr6_cox_hap1	hg18_refGene	exon	3413240	3413559	0	+	.	ID=NM_000500.;Parent=NM_000500;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32114061	32117398	0	+	.	ID=NM_001128590;Parent=NM_001128590;
Offending exons overlapped:
chr6	hg18_refGene	exon	32116625	32117398	0	+	.	ID=NM_001128590.;Parent=NM_001128590;
chr6_cox_hap1	hg18_refGene	exon	3413240	3413559	0	+	.	ID=NM_001128590.;Parent=NM_001128590;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32116911	32121883	0	-	.	ID=NM_032470;Parent=NM_032470;
Offending exons overlapped:
chr6	hg18_refGene	exon	32120761	32121883	0	-	.	ID=NM_032470.;Parent=NM_032470;
chr6_cox_hap1	hg18_refGene	exon	3416090	3416385	0	-	.	ID=NM_032470.;Parent=NM_032470;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32116911	32185129	0	-	.	ID=NM_019105;Parent=NM_019105;
Offending exons overlapped:
chr6	hg18_refGene	exon	32184936	32185129	0	-	.	ID=NM_019105.;Parent=NM_019105;
chr6_cox_hap1	hg18_refGene	exon	3416090	3416385	0	-	.	ID=NM_019105.;Parent=NM_019105;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32191023	32203995	0	-	.	ID=NM_001136153;Parent=NM_001136153;
Offending exons overlapped:
chr6	hg18_refGene	exon	32203881	32203995	0	-	.	ID=NM_001136153.;Parent=NM_001136153;
chr6_cox_hap1	hg18_refGene	exon	3490216	3490914	0	-	.	ID=NM_001136153.;Parent=NM_001136153;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32191023	32203995	0	-	.	ID=NM_004381;Parent=NM_004381;
Offending exons overlapped:
chr6	hg18_refGene	exon	32203872	32203995	0	-	.	ID=NM_004381.;Parent=NM_004381;
chr6_cox_hap1	hg18_refGene	exon	3490216	3490914	0	-	.	ID=NM_004381.;Parent=NM_004381;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32204462	32206045	0	-	.	ID=NM_022110;Parent=NM_022110;
Offending exons overlapped:
chr6	hg18_refGene	exon	32205850	32206045	0	-	.	ID=NM_022110.;Parent=NM_022110;
chr6_cox_hap1	hg18_refGene	exon	3503651	3504798	0	-	.	ID=NM_022110.;Parent=NM_022110;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32224118	32227698	0	-	.	ID=NM_030651;Parent=NM_030651;
Offending exons overlapped:
chr6	hg18_refGene	exon	32227564	32227698	0	-	.	ID=NM_030651.;Parent=NM_030651;
chr6_cox_hap1	hg18_refGene	exon	3523313	3524348	0	-	.	ID=NM_030651.;Parent=NM_030651;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32229279	32239430	0	+	.	ID=NM_138717;Parent=NM_138717;
Offending exons overlapped:
chr6	hg18_refGene	exon	32238562	32239430	0	+	.	ID=NM_138717.;Parent=NM_138717;
chr6_cox_hap1	hg18_refGene	exon	3528476	3528588	0	+	.	ID=NM_138717.;Parent=NM_138717;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32229600	32239430	0	+	.	ID=NM_005155;Parent=NM_005155;
Offending exons overlapped:
chr6	hg18_refGene	exon	32238562	32239430	0	+	.	ID=NM_005155.;Parent=NM_005155;
chr6_cox_hap1	hg18_refGene	exon	3528797	3529356	0	+	.	ID=NM_005155.;Parent=NM_005155;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32240383	32244040	0	+	.	ID=NM_030652;Parent=NM_030652;
Offending exons overlapped:
chr6	hg18_refGene	exon	32243665	32244040	0	+	.	ID=NM_030652.;Parent=NM_030652;
chr6_cox_hap1	hg18_refGene	exon	3539593	3539622	0	+	.	ID=NM_030652.;Parent=NM_030652;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32243967	32251877	0	-	.	ID=NM_006411;Parent=NM_006411;
Offending exons overlapped:
chr6	hg18_refGene	exon	32251569	32251877	0	-	.	ID=NM_006411.;Parent=NM_006411;
chr6_cox_hap1	hg18_refGene	exon	3543177	3544413	0	-	.	ID=NM_006411.;Parent=NM_006411;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32243967	32253820	0	-	.	ID=NM_032741;Parent=NM_032741;
Offending exons overlapped:
chr6	hg18_refGene	exon	32253756	32253820	0	-	.	ID=NM_032741.;Parent=NM_032741;
chr6_cox_hap1	hg18_refGene	exon	3543177	3544413	0	-	.	ID=NM_032741.;Parent=NM_032741;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32254140	32256548	0	+	.	ID=NM_006913;Parent=NM_006913;
Offending exons overlapped:
chr6	hg18_refGene	exon	32255984	32256548	0	+	.	ID=NM_006913.;Parent=NM_006913;
chr6_cox_hap1	hg18_refGene	exon	3553350	3553616	0	+	.	ID=NM_006913.;Parent=NM_006913;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32254210	32256545	0	+	.	ID=NR_003129;Parent=NR_003129;
Offending exons overlapped:
chr6	hg18_refGene	exon	32255984	32256545	0	+	.	ID=NR_003129.;Parent=NR_003129;
chr6_cox_hap1	hg18_refGene	exon	3553420	3553616	0	+	.	ID=NR_003129.;Parent=NR_003129;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32256724	32260001	0	-	.	ID=NM_001136;Parent=NM_001136;
Offending exons overlapped:
chr6	hg18_refGene	exon	32259926	32260001	0	-	.	ID=NM_001136.;Parent=NM_001136;
chr6_cox_hap1	hg18_refGene	exon	3555934	3556204	0	-	.	ID=NM_001136.;Parent=NM_001136;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32256724	32260001	0	-	.	ID=NM_172197;Parent=NM_172197;
Offending exons overlapped:
chr6	hg18_refGene	exon	32259926	32260001	0	-	.	ID=NM_172197.;Parent=NM_172197;
chr6_cox_hap1	hg18_refGene	exon	3555934	3556204	0	-	.	ID=NM_172197.;Parent=NM_172197;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32260488	32265941	0	-	.	ID=NM_002586;Parent=NM_002586;
Offending exons overlapped:
chr6	hg18_refGene	exon	32265450	32265941	0	-	.	ID=NM_002586.;Parent=NM_002586;
chr6_cox_hap1	hg18_refGene	exon	3559698	3561436	0	-	.	ID=NM_002586.;Parent=NM_002586;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32266521	32271278	0	-	.	ID=NM_022107;Parent=NM_022107;
Offending exons overlapped:
chr6	hg18_refGene	exon	32271181	32271278	0	-	.	ID=NM_022107.;Parent=NM_022107;
chr6_cox_hap1	hg18_refGene	exon	3565728	3566465	0	-	.	ID=NM_022107.;Parent=NM_022107;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32270598	32299822	0	-	.	ID=NM_004557;Parent=NM_004557;
Offending exons overlapped:
chr6	hg18_refGene	exon	32299611	32299822	0	-	.	ID=NM_004557.;Parent=NM_004557;
chr6_cox_hap1	hg18_refGene	exon	3569805	3571112	0	-	.	ID=NM_004557.;Parent=NM_004557;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32368453	32447634	0	-	.	ID=NM_006781;Parent=NM_006781;
Offending exons overlapped:
chr6	hg18_refGene	exon	32447449	32447634	0	-	.	ID=NM_006781.;Parent=NM_006781;
chr6_cox_hap1	hg18_refGene	exon	3667760	3669097	0	-	.	ID=NM_006781.;Parent=NM_006781;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32470491	32482878	0	-	.	ID=NM_019602;Parent=NM_019602;
Offending exons overlapped:
chr6	hg18_refGene	exon	32482800	32482878	0	-	.	ID=NM_019602.;Parent=NM_019602;
chr6_cox_hap1	hg18_refGene	exon	3769441	3769730	0	-	.	ID=NM_019602.;Parent=NM_019602;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32515625	32520802	0	+	.	ID=NM_019111;Parent=NM_019111;
Offending exons overlapped:
chr6	hg18_refGene	exon	32520407	32520802	0	+	.	ID=NM_019111.;Parent=NM_019111;
chr6_cox_hap1	hg18_refGene	exon	3814609	3814771	0	+	.	ID=NM_019111.;Parent=NM_019111;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32628468	32635757	0	-	.	ID=NR_001298;Parent=NR_001298;
Offending exons overlapped:
chr6	hg18_refGene	exon	32635571	32635757	0	-	.	ID=NR_001298.;Parent=NR_001298;
chr6_qbl_hap2	hg18_refGene	exon	3714100	3714208	0	-	.	ID=NR_001298.;Parent=NR_001298;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32654525	32665540	0	-	.	ID=NM_002124;Parent=NM_002124;
Offending exons overlapped:
chr6	hg18_refGene	exon	32665398	32665540	0	-	.	ID=NM_002124.;Parent=NM_002124;
chr6_cox_hap1	hg18_refGene	exon	3870632	3870783	0	-	.	ID=NM_002124.;Parent=NM_002124;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32817141	32823197	0	+	.	ID=NM_020056;Parent=NM_020056;
Offending exons overlapped:
chr6	hg18_refGene	exon	32822337	32823197	0	+	.	ID=NM_020056.;Parent=NM_020056;
chr6_cox_hap1	hg18_refGene	exon	4091391	4091530	0	+	.	ID=NM_020056.;Parent=NM_020056;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32831853	32839308	0	-	.	ID=NR_003937;Parent=NR_003937;
Offending exons overlapped:
chr6	hg18_refGene	exon	32839129	32839308	0	-	.	ID=NR_003937.;Parent=NR_003937;
chr6_cox_hap1	hg18_refGene	exon	4106104	4106472	0	-	.	ID=NR_003937.;Parent=NR_003937;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32888518	32892803	0	-	.	ID=NM_002120;Parent=NM_002120;
Offending exons overlapped:
chr6	hg18_refGene	exon	32892616	32892803	0	-	.	ID=NM_002120.;Parent=NM_002120;
chr6_cox_hap1	hg18_refGene	exon	4161397	4161885	0	-	.	ID=NM_002120.;Parent=NM_002120;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32897588	32914525	0	-	.	ID=NM_018833;Parent=NM_018833;
Offending exons overlapped:
chr6	hg18_refGene	exon	32914408	32914525	0	-	.	ID=NM_018833.;Parent=NM_018833;
chr6_cox_hap1	hg18_refGene	exon	4170467	4170952	0	-	.	ID=NM_018833.;Parent=NM_018833;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32901165	32914525	0	-	.	ID=NM_000544;Parent=NM_000544;
Offending exons overlapped:
chr6	hg18_refGene	exon	32914408	32914525	0	-	.	ID=NM_000544.;Parent=NM_000544;
chr6_cox_hap1	hg18_refGene	exon	4174043	4177667	0	-	.	ID=NM_000544.;Parent=NM_000544;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32916472	32919794	0	-	.	ID=NM_148919;Parent=NM_148919;
Offending exons overlapped:
chr6	hg18_refGene	exon	32919605	32919794	0	-	.	ID=NM_148919.;Parent=NM_148919;
chr6_cox_hap1	hg18_refGene	exon	4189349	4189679	0	-	.	ID=NM_148919.;Parent=NM_148919;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32916472	32920690	0	-	.	ID=NM_004159;Parent=NM_004159;
Offending exons overlapped:
chr6	hg18_refGene	exon	32920034	32920690	0	-	.	ID=NM_004159.;Parent=NM_004159;
chr6_cox_hap1	hg18_refGene	exon	4189349	4189679	0	-	.	ID=NM_004159.;Parent=NM_004159;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32920964	32929726	0	-	.	ID=NM_000593;Parent=NM_000593;
Offending exons overlapped:
chr6	hg18_refGene	exon	32928794	32929726	0	-	.	ID=NM_000593.;Parent=NM_000593;
chr6_cox_hap1	hg18_refGene	exon	4193841	4194417	0	-	.	ID=NM_000593.;Parent=NM_000593;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32929916	32935606	0	+	.	ID=NM_002800;Parent=NM_002800;
Offending exons overlapped:
chr6	hg18_refGene	exon	32935160	32935606	0	+	.	ID=NM_002800.;Parent=NM_002800;
chr6_cox_hap1	hg18_refGene	exon	4202793	4202921	0	+	.	ID=NM_002800.;Parent=NM_002800;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	32952233	32955827	0	+	.	ID=NR_027771;Parent=NR_027771;
Offending exons overlapped:
chr6	hg18_refGene	exon	32952233	32955827	0	+	.	ID=NR_027771.;Parent=NR_027771;
chr6_cox_hap1	hg18_refGene	exon	4225110	4228704	0	+	.	ID=NR_027771.;Parent=NR_027771;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33010393	33016795	0	-	.	ID=NM_002118;Parent=NM_002118;
Offending exons overlapped:
chr6	hg18_refGene	exon	33016508	33016795	0	-	.	ID=NM_002118.;Parent=NM_002118;
chr6_cox_hap1	hg18_refGene	exon	4283266	4283615	0	-	.	ID=NM_002118.;Parent=NM_002118;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33024369	33028877	0	-	.	ID=NM_006120;Parent=NM_006120;
Offending exons overlapped:
chr6	hg18_refGene	exon	33028704	33028877	0	-	.	ID=NM_006120.;Parent=NM_006120;
chr6_cox_hap1	hg18_refGene	exon	4297244	4297501	0	-	.	ID=NM_006120.;Parent=NM_006120;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33044415	33057260	0	+	.	ID=NM_005104;Parent=NM_005104;
Offending exons overlapped:
chr6	hg18_refGene	exon	33056337	33057260	0	+	.	ID=NM_005104.;Parent=NM_005104;
chr6_cox_hap1	hg18_refGene	exon	4317302	4317698	0	+	.	ID=NM_005104.;Parent=NM_005104;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33046656	33057260	0	+	.	ID=NM_001113182;Parent=NM_001113182;
Offending exons overlapped:
chr6	hg18_refGene	exon	33056337	33057260	0	+	.	ID=NM_001113182.;Parent=NM_001113182;
chr6_cox_hap1	hg18_refGene	exon	4319543	4319839	0	+	.	ID=NM_001113182.;Parent=NM_001113182;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33079938	33085367	0	-	.	ID=NM_002119;Parent=NM_002119;
Offending exons overlapped:
chr6	hg18_refGene	exon	33085210	33085367	0	-	.	ID=NM_002119.;Parent=NM_002119;
chr6_cox_hap1	hg18_refGene	exon	4352784	4355442	0	-	.	ID=NM_002119.;Parent=NM_002119;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33140772	33149356	0	-	.	ID=NM_033554;Parent=NM_033554;
Offending exons overlapped:
chr6	hg18_refGene	exon	33149226	33149356	0	-	.	ID=NM_033554.;Parent=NM_033554;
chr6_cox_hap1	hg18_refGene	exon	4413301	4413631	0	-	.	ID=NM_033554.;Parent=NM_033554;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33151738	33162954	0	+	.	ID=NM_002121;Parent=NM_002121;
Offending exons overlapped:
chr6	hg18_refGene	exon	33162294	33162954	0	+	.	ID=NM_002121.;Parent=NM_002121;
chr6_cox_hap1	hg18_refGene	exon	4424267	4424425	0	+	.	ID=NM_002121.;Parent=NM_002121;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33188271	33204868	0	+	.	ID=NR_001435;Parent=NR_001435;
Offending exons overlapped:
chr6	hg18_refGene	exon	33204820	33204868	0	+	.	ID=NR_001435.;Parent=NR_001435;
chr6_cox_hap1	hg18_refGene	exon	4460720	4460819	0	+	.	ID=NR_001435.;Parent=NR_001435;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33238447	33268223	0	-	.	ID=NM_080679;Parent=NM_080679;
Offending exons overlapped:
chr6	hg18_refGene	exon	33267914	33268223	0	-	.	ID=NM_080679.;Parent=NM_080679;
chr6_cox_hap1	hg18_refGene	exon	4510633	4511759	0	-	.	ID=NM_080679.;Parent=NM_080679;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33238447	33268223	0	-	.	ID=NM_080681;Parent=NM_080681;
Offending exons overlapped:
chr6	hg18_refGene	exon	33267914	33268223	0	-	.	ID=NM_080681.;Parent=NM_080681;
chr6_cox_hap1	hg18_refGene	exon	4510633	4511759	0	-	.	ID=NM_080681.;Parent=NM_080681;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33238447	33268223	0	-	.	ID=NM_080680;Parent=NM_080680;
Offending exons overlapped:
chr6	hg18_refGene	exon	33267914	33268223	0	-	.	ID=NM_080680.;Parent=NM_080680;
chr6_cox_hap1	hg18_refGene	exon	4510633	4511759	0	-	.	ID=NM_080680.;Parent=NM_080680;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33262202	33268223	0	-	.	ID=NM_001163771;Parent=NM_001163771;
Offending exons overlapped:
chr6	hg18_refGene	exon	33267914	33268223	0	-	.	ID=NM_001163771.;Parent=NM_001163771;
chr6_cox_hap1	hg18_refGene	exon	4534387	4534758	0	-	.	ID=NM_001163771.;Parent=NM_001163771;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33269343	33276410	0	-	.	ID=NM_021976;Parent=NM_021976;
Offending exons overlapped:
chr6	hg18_refGene	exon	33275997	33276410	0	-	.	ID=NM_021976.;Parent=NM_021976;
chr6_cox_hap1	hg18_refGene	exon	4541528	4542769	0	-	.	ID=NM_021976.;Parent=NM_021976;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33276581	33280192	0	+	.	ID=NM_001077516;Parent=NM_001077516;
Offending exons overlapped:
chr6	hg18_refGene	exon	33279296	33280192	0	+	.	ID=NM_001077516.;Parent=NM_001077516;
chr6_cox_hap1	hg18_refGene	exon	4548764	4548876	0	+	.	ID=NM_001077516.;Parent=NM_001077516;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33276581	33280192	0	+	.	ID=NM_006979;Parent=NM_006979;
Offending exons overlapped:
chr6	hg18_refGene	exon	33279296	33280192	0	+	.	ID=NM_006979.;Parent=NM_006979;
chr6_cox_hap1	hg18_refGene	exon	4548764	4549594	0	+	.	ID=NM_006979.;Parent=NM_006979;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33280397	33282585	0	+	.	ID=NM_014234;Parent=NM_014234;
Offending exons overlapped:
chr6	hg18_refGene	exon	33282393	33282585	0	+	.	ID=NM_014234.;Parent=NM_014234;
chr6_cox_hap1	hg18_refGene	exon	4552580	4552658	0	+	.	ID=NM_014234.;Parent=NM_014234;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33283590	33283699	0	+	.	ID=NR_029633;Parent=NR_029633;
Offending exons overlapped:
chr6	hg18_refGene	exon	33283590	33283699	0	+	.	ID=NR_029633.;Parent=NR_029633;
chr6_cox_hap1	hg18_refGene	exon	4555769	4555878	0	+	.	ID=NR_029633.;Parent=NR_029633;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33284264	33288477	0	+	.	ID=NM_002931;Parent=NM_002931;
Offending exons overlapped:
chr6	hg18_refGene	exon	33288053	33288477	0	+	.	ID=NM_002931.;Parent=NM_002931;
chr6_cox_hap1	hg18_refGene	exon	4556443	4556578	0	+	.	ID=NM_002931.;Parent=NM_002931;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33326027	33347640	0	-	.	ID=NM_022553;Parent=NM_022553;
Offending exons overlapped:
chr6	hg18_refGene	exon	33347341	33347640	0	-	.	ID=NM_022553.;Parent=NM_022553;
chr6_cox_hap1	hg18_refGene	exon	4598202	4598917	0	-	.	ID=NM_022553.;Parent=NM_022553;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33347830	33352259	0	+	.	ID=NM_022551;Parent=NM_022551;
Offending exons overlapped:
chr6	hg18_refGene	exon	33352146	33352259	0	+	.	ID=NM_022551.;Parent=NM_022551;
chr6_cox_hap1	hg18_refGene	exon	4619989	4620036	0	+	.	ID=NM_022551.;Parent=NM_022551;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33352895	33354580	0	+	.	ID=NM_003782;Parent=NM_003782;
Offending exons overlapped:
chr6	hg18_refGene	exon	33352895	33354580	0	+	.	ID=NM_003782.;Parent=NM_003782;
chr6_cox_hap1	hg18_refGene	exon	4625054	4626739	0	+	.	ID=NM_003782.;Parent=NM_003782;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33354858	33365282	0	-	.	ID=NM_005452;Parent=NM_005452;
Offending exons overlapped:
chr6	hg18_refGene	exon	33364857	33365282	0	-	.	ID=NM_005452.;Parent=NM_005452;
chr6_cox_hap1	hg18_refGene	exon	4627017	4627288	0	-	.	ID=NM_005452.;Parent=NM_005452;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33354858	33365282	0	-	.	ID=NM_001164267;Parent=NM_001164267;
Offending exons overlapped:
chr6	hg18_refGene	exon	33364857	33365282	0	-	.	ID=NM_001164267.;Parent=NM_001164267;
chr6_cox_hap1	hg18_refGene	exon	4627017	4627288	0	-	.	ID=NM_001164267.;Parent=NM_001164267;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33365356	33366689	0	+	.	ID=NM_014260;Parent=NM_014260;
Offending exons overlapped:
chr6	hg18_refGene	exon	33366471	33366689	0	+	.	ID=NM_014260.;Parent=NM_014260;
chr6_cox_hap1	hg18_refGene	exon	4637519	4637546	0	+	.	ID=NM_014260.;Parent=NM_014260;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33367410	33375154	0	-	.	ID=NR_028387;Parent=NR_028387;
Offending exons overlapped:
chr6	hg18_refGene	exon	33374625	33375154	0	-	.	ID=NR_028387.;Parent=NR_028387;
chr6_cox_hap1	hg18_refGene	exon	4639573	4640231	0	-	.	ID=NR_028387.;Parent=NR_028387;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33367410	33375154	0	-	.	ID=NM_004761;Parent=NM_004761;
Offending exons overlapped:
chr6	hg18_refGene	exon	33374625	33375154	0	-	.	ID=NM_004761.;Parent=NM_004761;
chr6_cox_hap1	hg18_refGene	exon	4639573	4640231	0	-	.	ID=NM_004761.;Parent=NM_004761;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33375452	33390142	0	-	.	ID=NM_172209;Parent=NM_172209;
Offending exons overlapped:
chr6	hg18_refGene	exon	33389760	33390142	0	-	.	ID=NM_172209.;Parent=NM_172209;
chr6_cox_hap1	hg18_refGene	exon	4647615	4649696	0	-	.	ID=NM_172209.;Parent=NM_172209;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33375452	33390142	0	-	.	ID=NM_003190;Parent=NM_003190;
Offending exons overlapped:
chr6	hg18_refGene	exon	33389760	33390142	0	-	.	ID=NM_003190.;Parent=NM_003190;
chr6_cox_hap1	hg18_refGene	exon	4647615	4649696	0	-	.	ID=NM_003190.;Parent=NM_003190;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33379390	33390142	0	-	.	ID=NM_172208;Parent=NM_172208;
Offending exons overlapped:
chr6	hg18_refGene	exon	33389760	33390142	0	-	.	ID=NM_172208.;Parent=NM_172208;
chr6_cox_hap1	hg18_refGene	exon	4651560	4651916	0	-	.	ID=NM_172208.;Parent=NM_172208;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33390161	33393490	0	-	.	ID=NM_005453;Parent=NM_005453;
Offending exons overlapped:
chr6	hg18_refGene	exon	33393408	33393490	0	-	.	ID=NM_005453.;Parent=NM_005453;
chr6_cox_hap1	hg18_refGene	exon	4662322	4664901	0	-	.	ID=NM_005453.;Parent=NM_005453;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33390161	33393697	0	-	.	ID=NM_001145338;Parent=NM_001145338;
Offending exons overlapped:
chr6	hg18_refGene	exon	33393633	33393697	0	-	.	ID=NM_001145338.;Parent=NM_001145338;
chr6_cox_hap1	hg18_refGene	exon	4662322	4664901	0	-	.	ID=NM_001145338.;Parent=NM_001145338;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33394313	33398771	0	-	.	ID=NR_024517;Parent=NR_024517;
Offending exons overlapped:
chr6	hg18_refGene	exon	33398617	33398771	0	-	.	ID=NR_024517.;Parent=NR_024517;
chr6_cox_hap1	hg18_refGene	exon	4666476	4666722	0	-	.	ID=NR_024517.;Parent=NR_024517;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33394313	33398771	0	-	.	ID=NM_001350;Parent=NM_001350;
Offending exons overlapped:
chr6	hg18_refGene	exon	33398617	33398771	0	-	.	ID=NM_001350.;Parent=NM_001350;
chr6_cox_hap1	hg18_refGene	exon	4666476	4666722	0	-	.	ID=NM_001350.;Parent=NM_001350;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33394313	33398771	0	-	.	ID=NM_001141969;Parent=NM_001141969;
Offending exons overlapped:
chr6	hg18_refGene	exon	33398617	33398771	0	-	.	ID=NM_001141969.;Parent=NM_001141969;
chr6_cox_hap1	hg18_refGene	exon	4666476	4666722	0	-	.	ID=NM_001141969.;Parent=NM_001141969;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33394313	33398771	0	-	.	ID=NM_001141970;Parent=NM_001141970;
Offending exons overlapped:
chr6	hg18_refGene	exon	33398617	33398771	0	-	.	ID=NM_001141970.;Parent=NM_001141970;
chr6_cox_hap1	hg18_refGene	exon	4666476	4666722	0	-	.	ID=NM_001141970.;Parent=NM_001141970;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33440491	33442117	0	-	.	ID=NR_001444;Parent=NR_001444;
Offending exons overlapped:
chr6	hg18_refGene	exon	33440491	33442117	0	-	.	ID=NR_001444.;Parent=NR_001444;
chr6_cox_hap1	hg18_refGene	exon	4712654	4714280	0	-	.	ID=NR_001444.;Parent=NR_001444;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	33467291	33485677	0	+	.	ID=NM_002263;Parent=NM_002263;
Offending exons overlapped:
chr6	hg18_refGene	exon	33485401	33485677	0	+	.	ID=NM_002263.;Parent=NM_002263;
chr6_qbl_hap2	hg18_refGene	exon	4545487	4545948	0	+	.	ID=NM_002263.;Parent=NM_002263;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	167928070	167940388	0	-	.	ID=NR_026773;Parent=NR_026773;
Offending exons overlapped:
chr6	hg18_refGene	exon	167940138	167940388	0	-	.	ID=NR_026773.;Parent=NR_026773;
chr6_random	hg18_refGene	exon	771904	772863	0	-	.	ID=NR_026773.;Parent=NR_026773;
Error: bad transcript annotation:
chr6	hg18_refGene	mRNA	167967419	167970325	0	-	.	ID=NR_027906;Parent=NR_027906;
Offending exons overlapped:
chr6	hg18_refGene	exon	167968932	167970325	0	-	.	ID=NR_027906.;Parent=NR_027906;
chr6_random	hg18_refGene	exon	811286	812202	0	-	.	ID=NR_027906.;Parent=NR_027906;
Error: bad transcript annotation:
chr8	hg18_refGene	mRNA	145509055	145521375	0	-	.	ID=NM_012079;Parent=NM_012079;
Offending exons overlapped:
chr8	hg18_refGene	exon	145520908	145521375	0	-	.	ID=NM_012079.;Parent=NM_012079;
chr8_random	hg18_refGene	exon	408763	409230	0	+	.	ID=NM_012079.;Parent=NM_012079;
Error: bad transcript annotation:
chr8	hg18_refGene	mRNA	145525262	145530751	0	-	.	ID=NM_031309;Parent=NM_031309;
Offending exons overlapped:
chr8	hg18_refGene	exon	145530525	145530751	0	-	.	ID=NM_031309.;Parent=NM_031309;
chr8_random	hg18_refGene	exon	399387	399613	0	+	.	ID=NM_031309.;Parent=NM_031309;
Error: bad transcript annotation:
chr9	hg18_refGene	mRNA	139234528	139235596	0	-	.	ID=NM_031297;Parent=NM_031297;
Offending exons overlapped:
chr9	hg18_refGene	exon	139234528	139235596	0	-	.	ID=NM_031297.;Parent=NM_031297;
chr9_random	hg18_refGene	exon	1126638	1127706	0	+	.	ID=NM_031297.;Parent=NM_031297;
Error: bad transcript annotation:
chr9	hg18_refGene	mRNA	139239465	139240583	0	+	.	ID=NM_199001;Parent=NM_199001;
Offending exons overlapped:
chr9	hg18_refGene	exon	139239887	139240583	0	+	.	ID=NM_199001.;Parent=NM_199001;
chr9_random	hg18_refGene	exon	1130468	1131164	0	-	.	ID=NM_199001.;Parent=NM_199001;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	132991	160020	0	+	.	ID=NR_028057;Parent=NR_028057;
Offending exons overlapped:
chrX	hg18_refGene	exon	159260	160020	0	+	.	ID=NR_028057.;Parent=NR_028057;
chrY	hg18_refGene	exon	132991	133061	0	+	.	ID=NR_028057.;Parent=NR_028057;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	138061	160020	0	+	.	ID=NM_018390;Parent=NM_018390;
Offending exons overlapped:
chrX	hg18_refGene	exon	155764	160020	0	+	.	ID=NM_018390.;Parent=NM_018390;
chrY	hg18_refGene	exon	138061	138351	0	+	.	ID=NM_018390.;Parent=NM_018390;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	214669	267690	0	-	.	ID=NM_013239;Parent=NM_013239;
Offending exons overlapped:
chrX	hg18_refGene	exon	267103	267690	0	-	.	ID=NM_013239.;Parent=NM_013239;
chrY	hg18_refGene	exon	214669	215252	0	-	.	ID=NM_013239.;Parent=NM_013239;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	505079	527558	0	+	.	ID=NM_000451;Parent=NM_000451;
Offending exons overlapped:
chrX	hg18_refGene	exon	525126	527558	0	+	.	ID=NM_000451.;Parent=NM_000451;
chrY	hg18_refGene	exon	505079	505337	0	+	.	ID=NM_000451.;Parent=NM_000451;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	505079	540146	0	+	.	ID=NM_006883;Parent=NM_006883;
Offending exons overlapped:
chrX	hg18_refGene	exon	539520	540146	0	+	.	ID=NM_006883.;Parent=NM_006883;
chrY	hg18_refGene	exon	505079	505337	0	+	.	ID=NM_006883.;Parent=NM_006883;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1274887	1291527	0	-	.	ID=NM_001012288;Parent=NM_001012288;
Offending exons overlapped:
chrX_random	hg18_refGene	exon	1687438	1687565	0	+	.	ID=NM_001012288.;Parent=NM_001012288;
chrY	hg18_refGene	exon	1274887	1275014	0	-	.	ID=NM_001012288.;Parent=NM_001012288;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1274894	1291530	0	-	.	ID=NM_022148;Parent=NM_022148;
Offending exons overlapped:
chrX_random	hg18_refGene	exon	1687438	1687558	0	+	.	ID=NM_022148.;Parent=NM_022148;
chrY	hg18_refGene	exon	1274894	1275014	0	-	.	ID=NM_022148.;Parent=NM_022148;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1347693	1384711	0	+	.	ID=NM_001161531;Parent=NM_001161531;
Offending exons overlapped:
chrX	hg18_refGene	exon	1384521	1384711	0	+	.	ID=NM_001161531.;Parent=NM_001161531;
chrY	hg18_refGene	exon	1347693	1347772	0	+	.	ID=NM_001161531.;Parent=NM_001161531;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1347693	1388828	0	+	.	ID=NM_172249;Parent=NM_172249;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NM_172249.;Parent=NM_172249;
chrY	hg18_refGene	exon	1347693	1347772	0	+	.	ID=NM_172249.;Parent=NM_172249;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1347693	1388828	0	+	.	ID=NM_172246;Parent=NM_172246;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NM_172246.;Parent=NM_172246;
chrY	hg18_refGene	exon	1347693	1347772	0	+	.	ID=NM_172246.;Parent=NM_172246;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1347693	1388828	0	+	.	ID=NM_001161532;Parent=NM_001161532;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NM_001161532.;Parent=NM_001161532;
chrY	hg18_refGene	exon	1347693	1347772	0	+	.	ID=NM_001161532.;Parent=NM_001161532;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1347693	1388828	0	+	.	ID=NM_172245;Parent=NM_172245;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NM_172245.;Parent=NM_172245;
chrY	hg18_refGene	exon	1347693	1347772	0	+	.	ID=NM_172245.;Parent=NM_172245;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1347693	1388828	0	+	.	ID=NM_006140;Parent=NM_006140;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NM_006140.;Parent=NM_006140;
chrY	hg18_refGene	exon	1347693	1347772	0	+	.	ID=NM_006140.;Parent=NM_006140;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1347693	1388828	0	+	.	ID=NM_001161529;Parent=NM_001161529;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NM_001161529.;Parent=NM_001161529;
chrY	hg18_refGene	exon	1347693	1347772	0	+	.	ID=NM_001161529.;Parent=NM_001161529;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1347693	1388828	0	+	.	ID=NR_027760;Parent=NR_027760;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NR_027760.;Parent=NR_027760;
chrY	hg18_refGene	exon	1347693	1347772	0	+	.	ID=NR_027760.;Parent=NR_027760;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1361571	1388828	0	+	.	ID=NM_001161530;Parent=NM_001161530;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NM_001161530.;Parent=NM_001161530;
chrY	hg18_refGene	exon	1361571	1361672	0	+	.	ID=NM_001161530.;Parent=NM_001161530;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1361571	1388828	0	+	.	ID=NM_172247;Parent=NM_172247;
Offending exons overlapped:
chrX	hg18_refGene	exon	1388295	1388828	0	+	.	ID=NM_172247.;Parent=NM_172247;
chrY	hg18_refGene	exon	1361571	1361672	0	+	.	ID=NM_172247.;Parent=NM_172247;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1415509	1461582	0	+	.	ID=NM_002183;Parent=NM_002183;
Offending exons overlapped:
chrX	hg18_refGene	exon	1461284	1461582	0	+	.	ID=NM_002183.;Parent=NM_002183;
chrY	hg18_refGene	exon	1415509	1415819	0	+	.	ID=NM_002183.;Parent=NM_002183;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1465045	1471039	0	-	.	ID=NM_001636;Parent=NM_001636;
Offending exons overlapped:
chrX	hg18_refGene	exon	1470792	1471039	0	-	.	ID=NM_001636.;Parent=NM_001636;
chrY	hg18_refGene	exon	1465045	1465652	0	-	.	ID=NM_001636.;Parent=NM_001636;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1479424	1492478	0	+	.	ID=NR_026710;Parent=NR_026710;
Offending exons overlapped:
chrX	hg18_refGene	exon	1491636	1492478	0	+	.	ID=NR_026710.;Parent=NR_026710;
chrY	hg18_refGene	exon	1479424	1479479	0	+	.	ID=NR_026710.;Parent=NR_026710;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1479424	1494313	0	+	.	ID=NR_026711;Parent=NR_026711;
Offending exons overlapped:
chrX	hg18_refGene	exon	1493636	1494313	0	+	.	ID=NR_026711.;Parent=NR_026711;
chrY	hg18_refGene	exon	1479424	1479479	0	+	.	ID=NR_026711.;Parent=NR_026711;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1482032	1531870	0	-	.	ID=NM_004192;Parent=NM_004192;
Offending exons overlapped:
chrX	hg18_refGene	exon	1531641	1531870	0	-	.	ID=NM_004192.;Parent=NM_004192;
chrY	hg18_refGene	exon	1482032	1482382	0	-	.	ID=NM_004192.;Parent=NM_004192;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1482032	1531870	0	-	.	ID=NM_001173474;Parent=NM_001173474;
Offending exons overlapped:
chrX	hg18_refGene	exon	1531641	1531870	0	-	.	ID=NM_001173474.;Parent=NM_001173474;
chrY	hg18_refGene	exon	1482032	1482382	0	-	.	ID=NM_001173474.;Parent=NM_001173474;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1482032	1532655	0	-	.	ID=NM_001173473;Parent=NM_001173473;
Offending exons overlapped:
chrX	hg18_refGene	exon	1532511	1532655	0	-	.	ID=NM_001173473.;Parent=NM_001173473;
chrY	hg18_refGene	exon	1482032	1482382	0	-	.	ID=NM_001173473.;Parent=NM_001173473;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1541468	1616037	0	-	.	ID=NM_178129;Parent=NM_178129;
Offending exons overlapped:
chrX	hg18_refGene	exon	1615814	1616037	0	-	.	ID=NM_178129.;Parent=NM_178129;
chrY	hg18_refGene	exon	1541468	1545475	0	-	.	ID=NM_178129.;Parent=NM_178129;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1670486	1681405	0	+	.	ID=NR_027383;Parent=NR_027383;
Offending exons overlapped:
chrX	hg18_refGene	exon	1679552	1681405	0	+	.	ID=NR_027383.;Parent=NR_027383;
chrY	hg18_refGene	exon	1670486	1670662	0	+	.	ID=NR_027383.;Parent=NR_027383;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1670486	1681411	0	+	.	ID=NM_005088;Parent=NM_005088;
Offending exons overlapped:
chrX	hg18_refGene	exon	1679552	1681411	0	+	.	ID=NM_005088.;Parent=NM_005088;
chrY	hg18_refGene	exon	1670486	1670662	0	+	.	ID=NM_005088.;Parent=NM_005088;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1674348	1721974	0	+	.	ID=NM_004043;Parent=NM_004043;
Offending exons overlapped:
chrX	hg18_refGene	exon	1721696	1721974	0	+	.	ID=NM_004043.;Parent=NM_004043;
chrY	hg18_refGene	exon	1674348	1674425	0	+	.	ID=NM_004043.;Parent=NM_004043;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1693941	1721973	0	+	.	ID=NM_001171038;Parent=NM_001171038;
Offending exons overlapped:
chrX	hg18_refGene	exon	1721696	1721973	0	+	.	ID=NM_001171038.;Parent=NM_001171038;
chrY	hg18_refGene	exon	1693941	1694161	0	+	.	ID=NM_001171038.;Parent=NM_001171038;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	1694026	1721973	0	+	.	ID=NM_001171039;Parent=NM_001171039;
Offending exons overlapped:
chrX	hg18_refGene	exon	1721696	1721973	0	+	.	ID=NM_001171039.;Parent=NM_001171039;
chrY	hg18_refGene	exon	1694026	1694161	0	+	.	ID=NM_001171039.;Parent=NM_001171039;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2147553	2429015	0	-	.	ID=NM_145177;Parent=NM_145177;
Offending exons overlapped:
chrX	hg18_refGene	exon	2428858	2429015	0	-	.	ID=NM_145177.;Parent=NM_145177;
chrY	hg18_refGene	exon	2147553	2149270	0	-	.	ID=NM_145177.;Parent=NM_145177;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2414455	2428580	0	-	.	ID=NM_001171135;Parent=NM_001171135;
Offending exons overlapped:
chrX	hg18_refGene	exon	2428352	2428580	0	-	.	ID=NM_001171135.;Parent=NM_001171135;
chrY	hg18_refGene	exon	2414455	2418813	0	-	.	ID=NM_001171135.;Parent=NM_001171135;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2414455	2429008	0	-	.	ID=NM_001171136;Parent=NM_001171136;
Offending exons overlapped:
chrX	hg18_refGene	exon	2428858	2429008	0	-	.	ID=NM_001171136.;Parent=NM_001171136;
chrY	hg18_refGene	exon	2414455	2418813	0	-	.	ID=NM_001171136.;Parent=NM_001171136;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2414455	2429008	0	-	.	ID=NM_004729;Parent=NM_004729;
Offending exons overlapped:
chrX	hg18_refGene	exon	2428858	2429008	0	-	.	ID=NM_004729.;Parent=NM_004729;
chrY	hg18_refGene	exon	2414455	2418810	0	-	.	ID=NM_004729.;Parent=NM_004729;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2537306	2566369	0	+	.	ID=NR_033381;Parent=NR_033381;
Offending exons overlapped:
chrX	hg18_refGene	exon	2566015	2566369	0	+	.	ID=NR_033381.;Parent=NR_033381;
chrY	hg18_refGene	exon	2537306	2537522	0	+	.	ID=NR_033381.;Parent=NR_033381;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2537306	2585270	0	+	.	ID=NR_033380;Parent=NR_033380;
Offending exons overlapped:
chrX	hg18_refGene	exon	2583068	2585270	0	+	.	ID=NR_033380.;Parent=NR_033380;
chrY	hg18_refGene	exon	2537306	2537522	0	+	.	ID=NR_033380.;Parent=NR_033380;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2619228	2669350	0	+	.	ID=NM_001122898;Parent=NM_001122898;
Offending exons overlapped:
chrX	hg18_refGene	exon	2668820	2669350	0	+	.	ID=NM_001122898.;Parent=NM_001122898;
chrY	hg18_refGene	exon	2619228	2619468	0	+	.	ID=NM_001122898.;Parent=NM_001122898;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2619228	2669350	0	+	.	ID=NM_002414;Parent=NM_002414;
Offending exons overlapped:
chrX	hg18_refGene	exon	2668820	2669350	0	+	.	ID=NM_002414.;Parent=NM_002414;
chrY	hg18_refGene	exon	2619228	2619468	0	+	.	ID=NM_002414.;Parent=NM_002414;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	2680337	2703037	0	+	.	ID=NR_003254;Parent=NR_003254;
Offending exons overlapped:
chrX	hg18_refGene	exon	2702757	2703037	0	+	.	ID=NR_003254.;Parent=NR_003254;
chrY	hg18_refGene	exon	2680337	2680376	0	+	.	ID=NR_003254.;Parent=NR_003254;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	77110114	77111791	0	-	.	ID=NM_001029891;Parent=NM_001029891;
Offending exons overlapped:
chrX	hg18_refGene	exon	77110114	77111791	0	-	.	ID=NM_001029891.;Parent=NM_001029891;
chrX_random	hg18_refGene	exon	1324940	1326617	0	-	.	ID=NM_001029891.;Parent=NM_001029891;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	77271901	77281835	0	-	.	ID=NM_015975;Parent=NM_015975;
Offending exons overlapped:
chrX	hg18_refGene	exon	77281714	77281835	0	-	.	ID=NM_015975.;Parent=NM_015975;
chrX_random	hg18_refGene	exon	1383007	1383128	0	+	.	ID=NM_015975.;Parent=NM_015975;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	154650645	154665311	0	+	.	ID=NM_005840;Parent=NM_005840;
Offending exons overlapped:
chrX	hg18_refGene	exon	154656622	154665311	0	+	.	ID=NM_005840.;Parent=NM_005840;
chrY	hg18_refGene	exon	57509845	57510192	0	+	.	ID=NM_005840.;Parent=NM_005840;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	154764141	154826626	0	+	.	ID=NM_005638;Parent=NM_005638;
Offending exons overlapped:
chrX	hg18_refGene	exon	154824741	154826626	0	+	.	ID=NM_005638.;Parent=NM_005638;
chrY	hg18_refGene	exon	57623341	57623505	0	+	.	ID=NM_005638.;Parent=NM_005638;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	154764141	154826626	0	+	.	ID=NM_001145149;Parent=NM_001145149;
Offending exons overlapped:
chrX	hg18_refGene	exon	154824741	154826626	0	+	.	ID=NM_001145149.;Parent=NM_001145149;
chrY	hg18_refGene	exon	57623341	57623505	0	+	.	ID=NM_001145149.;Parent=NM_001145149;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	154880440	154893676	0	+	.	ID=NR_024033;Parent=NR_024033;
Offending exons overlapped:
chrX	hg18_refGene	exon	154892675	154893676	0	+	.	ID=NR_024033.;Parent=NR_024033;
chrY	hg18_refGene	exon	57739640	57739846	0	+	.	ID=NR_024033.;Parent=NR_024033;
Error: bad transcript annotation:
chrX	hg18_refGene	mRNA	154880440	154893676	0	+	.	ID=NM_002186;Parent=NM_002186;
Offending exons overlapped:
chrX	hg18_refGene	exon	154892675	154893676	0	+	.	ID=NM_002186.;Parent=NM_002186;
chrY	hg18_refGene	exon	57739640	57739846	0	+	.	ID=NM_002186.;Parent=NM_002186;
Extracted 1321750 junctions from /projects/NBL/reference_files/UCSC/all.gtf.gff3