Gnodes DNA Depth Chromosome Plots: DNA-xCopy and Major Components

Snippets of chromosome plot starts, with graph of XCOPY, DUP duplicated DNA, CDS coding gene, TE Transposon, and RPT simple repeats as percent of spans.
XCOPY is DNA copy depth divided by standard of Unique Conserved Gene copy depth, with black bar at 1. Deficit (left) and Excess (right of 1-bar) depths are visible as red graph. Excess depths suggest span is under-assembled, seen most often for RPT and DUP regions, though mis-mapping of duplicate DNA may account for some discrepancy.

Arabidopsis thaliana: 2018.TAIR, 2020.Max Planck assemblies

Ara.th. 2018.TAIR Chr Depth Plot	Ara.th. 2020.Max Planck Chr Depth Plot

Ara.th. TAIR assembly has a -30% deficit in DNA spans, notably including genes with 2-9 copies. 2020Max assembly, though larger by 10 Mb, has greater deficits including large missing gene DNA.

Drosophila mel.r6, and mel.2020.pi2 assemblies

Dro.mel. Rel 6 Chr Depth Plot	Dro.mel. 2020 Pi2 Chr Depth Plot

Dros. melanogaster Release 6 assembly (drmel6r) has a noticable deficit of -17%, or 30 Megabases. Recent Dros. mel. 2020 (drmel20, Pi2) and Dros. pseudoobscura 2020 (drpse20) assemblies are at zero deficit, within measurement error. In drmel20pi2 however, XCOPY variation on the chromosomes is higher than in drmel6r, suggesting some errors in this new assembly. The drmel6r assembly has many un-located scaffolds with a high XCOPY variation, not shown, that account for the noticable deficit in assembly size.

Developed at the Genome Informatics Lab of Indiana University Biology Department