The genomic landscape of a HeLa cell line. The genomic landscape of a HeLa cell line. (A) Circos plot (Krzywinski et al. 2009) of the HeLa genome with tracks representing read depth (100 kb-binned coverage), CN (color gradient from light green for CN1 to dark red for CN10), zygosity (pink: heterozygous; purple: homozygous), SNV density (1-Mb binned SNV count; darker blue for greater density), and translocation calls (colored arcs based on paired-end sequencing data: light blue; mate pair data: light green; both datasets: orange). (B) Histogram of called CN across the genome in percent. CN 0 corresponds to coverage less than half of the expected value for CN 1. A CN value of “NA” means no call could be made with confidence ≥0.95 (see Materials and Methods). (C) Overview of sequence variation in HeLa. Numbers of SNV and indel calls in HeLa, classified by overlap with dbSNP and the 1000 Genomes Project (dbSNP137). The y-axis shows the counts on a logarithmic scale. The four different classes of events represented on the x-axis are homozygous (“Hom.”) and heterozygous (“Het.”) SNVs and indels. (D) Variation observed in HeLa protein-coding genes relative to the human reference. Number of protein-coding genes containing SNVs, nonsynonymous SNVs, and damaging non-synonymous mutations [predicted by SIFT (Ng and Henikoff 2003)]. Jonathan J. M. Landry et al. G3 2013;3:1213-1224 ©2013 by Genetics Society of America