Table 3.

Segregation analysis for 10-Mb region on chromosome 20 in the CEU trio of the 1000 Genomes Project

Indels were called in daughter and parents independently from Illumina data only. The indels that were called in the daughter but not in the parents (defined as the nonsegregating indels in the third and fourth columns) were validated using the 13.7X 454 data available for the daughter. We considered three different calling thresholds for VarScan, with q10 and q20 corresponding to 90% and 99% confidence thresholds, respectively.