All statistics are based on contigs of size >= 3000 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). Assembly abyss_scaffolds.all abyss_scaffolds.all_broken # contigs (>= 0 bp) 1388378 - # contigs (>= 1000 bp) 6371 - # contigs (>= 5000 bp) 2271 131515 # contigs (>= 10000 bp) 1701 82583 # contigs (>= 25000 bp) 1171 28693 # contigs (>= 50000 bp) 941 7009 Total length (>= 0 bp) 3107092178 - Total length (>= 1000 bp) 2772509182 - Total length (>= 5000 bp) 2764469504 2445648576 Total length (>= 10000 bp) 2760375817 2092930008 Total length (>= 25000 bp) 2751935307 1239980905 Total length (>= 50000 bp) 2743726564 494877822 # contigs 2969 265960 Largest contig 35633446 263849 Total length 2767277996 2710395163 Reference length 3088269832 3088269832 Reference GC (%) 40.87 40.87 N50 8467051 22523 NG50 6983694 18821 N75 3797956 10859 NG75 2497067 6821 L50 98 33547 LG50 119 42728 L75 222 76814 LG75 299 109471 # misassemblies 580 141 # misassembled contigs 320 135 Misassembled contigs length 822300286 2934673 # local misassemblies 5013 1291 # scaffold gap ext. mis. 218 - # scaffold gap loc. mis. 65001 - # possible TEs 188 18 # unaligned mis. contigs 50 47 # unaligned contigs 332 + 906 part 20587 + 1264 part Unaligned length 13711769 14087624 Genome fraction (%) 92.340 91.377 Duplication ratio 1.015 1.004 # N's per 100 kbp 1974.11 5.28 # mismatches per 100 kbp 111.66 95.83 # indels per 100 kbp 29.35 23.13 Largest alignment 30890222 263815 Total aligned length 2709385682 2694647361 NA50 6635272 22455 NGA50 5460968 18763 NA75 3054180 10794 NGA75 1904102 6736 LA50 116 33618 LGA50 143 42830 LA75 269 77083 LGA75 370 110043