hg19KIndel: ethnicity normalized human reference genome

BMC Genomics

Table 5 Variant comparison for whole exome sequencing samples across three different versions of human genome

Sample	Genome		Variant class	Total Calls I	Total Calls II	Variant count			% false positives in I	% false negatives in I
Sample	I	II	Variant class	Total Calls I	Total Calls II	common	Unique to I	Unique to II	% false positives in I	% false negatives in I
NA12878	hg19	hg19K	SNP	43,313	33,064	30,046	13,267	3018	30.630	9.127
	hg19	hg19K	Indel	4251	4245	4191	60	54	1.411	1.272
	hg19	hg19KIndel	SNP	43,313	33,023	29,970	13,343	3053	30.803	9.245
	hg19	hg19KIndel	Indel	4251	3202	2827	1424	375	33.498	11.788
	hg19K	hg19KIndel	SNP	33,064	33,023	32,967	97	56	0.293	0.169
	hg19K	hg19KIndel	Indel	4245	3202	2863	1382	339	32.555	10.657
In house whole exome data	hg19	hg19K	SNP	45,285	33,700	30,633	14,652	3067	32.35	9.10
	hg19	hg19K	Indel	4741	4740	4680	61	60	1.28	1.26
	hg19	hg19KIndel	SNP	45,285	33,673	30,563	14,722	3110	32.50	9.24
	hg19	hg19KIndel	Indel	4741	3494	3090	1651	404	34.82	11.65
	hg19K	hg19KIndel	SNP	33,700	33,673	33,602	98	71	0.29	0.21
	hg19K	hg19KIndel	Indel	4740	3494	3122	1618	372	34.13	10.73

ISSN: 1471-2164