ntSynt Report — Populus poplars

Assembly statistics

Statistic	Value
Number of assemblies	34
Range of number of chromosomes	19 – 38
Genome size range (Mbp)	382.3 – 784.6

Source: Populus_poplars_assemblies/Populus_poplars_abyss_fac-summary.tsv

Synteny block statistics

Statistic	Value
Number of blocks	55
Average synteny coverage (%)	0.61
Synteny coverage of smallest genome (%)	0.68
N50 length of synteny blocks (bp)	127,764

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

Reasons for synteny block discontinuities

Synteny block discontinuity reason	Count
id_change	46
indel	6
ori_change	2

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

Populus_poplars_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/Populus_poplars_ribbon-plot_tree.html