Table 1

Summary information from mapping and assembly of three genomes. All variations are with respect to the National Center for Biotechnology Information (NCBI) version 36 human genome reference assembly. Novel variations were ascertained by comparison to dbSNP [JDW, release 126; NA18507 (6), release 128; all other genomes, release 129]. NA18507 and NA19240 are Yoruban HapMap samples, which may explain the number of SNPs and novelty rates. In partially called regions of the genome, one allele could be called confidently but not the other. The high call rate in NA19240 reflects reduced library bias (fig. S5).

SampleMapped sequence (Gb)Average coverage depth (fold)Percent of genome calledSNPsIndelsInsertion: deletion ratio
FullyPartiallyTotalNovel TotalNovel
Genomes sequenced by Complete Genomics
NA07022 (35)2418791%2%3,076,86910%337,63537%1.0
NA19240 (36)1786395%1%4,042,80119%496,19442%0.96
NA20431 (37)1244586%3%2,905,51710%269,79437%1.0
Genomes previously published
NA18507 (6)131464,139,19626%404,41650%0.77
NA18507 (9)8731*3,866,08519%226,52933%0.72
JCV (3)2173,213,40115%851,575
JDW (4)217-–3,322,09318%222,71851%0.4

*This is 18x when constrained to nonduplicated and properly mated reads, which were those used for variant calling.