Fig. 9
From: False gene and chromosome losses in genome assemblies caused by GC content variation and repeats
Genomic regions that failed to be assembled in chromosome-level scaffolds of the VGP zebra finch primary assembly (bTaeGut1_v1.p). a Alignment between the previous, VGP Trio-based, VGP alternate and VGP primary assemblies for a 2.7 Mb end of chromosome 19. Gray, chromosome-level scaffolds. Black arrows, annotated genes. Links between gray bars indicate the alignment between each scaffold. b, GC- and repeat content of the 2.7 Mb region missing in the VGP primary assembly. Gray, dark gray, and red indicate GC and repeat content calculated from 10-kbp consecutive blocks extracted from the whole genome of a VGP trio-based assembly, chromosome 19, and the 2.7 Mb end of chromosome 19, respectively. c Repeat profile of the 2.7-Mb region missing in the VGP primary assembly. Repeat content was calculated from 10-kbp consecutive blocks extracted from the whole genome (gray), chromosome 19 (dark gray), or 2.7 Mb end of chromosome 19 (red) of the VGP Trio-based assembly. Bars and error bars indicate the mean and S.D. of repeat content of the blocks (****: p < 0.0001, ***: p < 0.001, **: p < 0.01, *: p < 0.05. p-values were calculated by ANOVA)