I analysed the TGAC KW1 assembly of Hymenoscyphus pseudoalbidus / Chalara fraxinea to display various features of the assembly. Click for larger image
- (outer black ring) – scaffolds of length >= 10 kbp
- (blue stacks) – gene models
- (blue heatmap) – gene density in 10 kbp windows
- (line plot) – aligned distance between paired end read for library with 196 bp insert size (< 31 bp – 5th percentile – rendered in orange, > 351 bp – 95th percentile – rendered in blue)
- (line plot) – aligned distance between paired end read for library with 570 bp insert size (< 265 bp – 5th percentile – rendered in orange, > 2313 bp – 95th percentile – rendered in blue) Thresholds calculated as per (https://github.com/danmaclean/h_pseu_analysis/blob/master/circos/scripts/assess_insert_size_distributions.md)
- (pink line plot) – uniquely mapped read covereage. Maximum plotted = 300, minimum plotted = 80
- (pink line plot) – GC percent. Black line = 50% GC, light grey area = 50% – 30 % GC, dark grey area = > 30% GC.
- Maximum plotted = 60% GC, minimum plotted = 20% GC
- (green stacks) – Repeat Masker matches.
The genome assembly contains numerous low GC, high coverage, repeat rich regions, with low overall gene density. This suggests an assembly with collapsed repeats of a genome that is overall rich in repeats.