ntSynt Report — Apis bees

Assembly statistics

Statistic	Value
Number of assemblies	11
Range of number of chromosomes	16 – 16
Genome size range (Mbp)	199.7 – 232.1

Source: Apis_bees_assemblies/Apis_bees_abyss_fac-summary.tsv

Synteny block statistics

Statistic	Value
Number of blocks	437
Average synteny coverage (%)	87.28
Synteny coverage of smallest genome (%)	88.61
N50 length of synteny blocks (bp)	887,409

Source: ntSynt.k24.w1000.synteny_blocks.stats.tsv

Reasons for synteny block discontinuities

Synteny block discontinuity reason	Count
ori_change	259
inconsistent_order	66
indel	58
id_change	52
merge	1

Source: ntSynt.k24.w1000.discontinuity_reasons.tsv

Mash divergence distributions

Pairwise mash distances across full-genome, syntenic, and non-syntenic regions. Wilcoxon signed-rank test p-value shown between syntenic and non-syntenic distributions. Interactive — hover over a point to see the genome pair. Source: mash/mash_divergence_boxplot.html

Synteny ribbon plot

Apis_bees_ribbon-plot_tree

ntSynt-viz ribbon plot showing synteny blocks across all assemblies. Nuclear genome tree included in ribbon plot. Interactive — hover to highlight, click to pin tooltips. Source: ntsynt-viz/Apis_bees_ribbon-plot_tree.html