hg19KIndel: ethnicity normalized human reference genome

BMC Genomics

Table 4 Variant comparison for WGS 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	3,691,042	2,859,214	2,624,382	1,066,660	23,482	28.89	8.21
	hg19	hg19K	Indel	809,628	807,394	789,612	20,014	17,782	2.47	2.20
	hg19	hg19KIndel	SNP	3,691,042	2,852,155	2,611,050	1,079,992	241,105	29.26	8.46
	hg19	hg19KIndel	Indel	809,628	651,931	570,962	238,666	80,969	29.48	12.53
	hg19K	hg19KIndel	SNP	2,859,214	2,852,155	2,837,316	21,898	14,839	0.76	0.52
	hg19K	hg19KIndel	Indel	807,394	651,931	582,100	225,294	69,831	27.90	10.80
In house Whole genome sample	hg19	hg19K	SNP	3,652,081	2,788,319	2,551,695	1,100,385	236,623	30.13	8.48
	hg19	hg19K	Indel	665,692	664,663	650,704	14,988	13,959	2.25	2.10
	hg19	hg19KIndel	SNP	3,652,081	2,783,025	2,541,407	1,110,674	241,618	30.41	8.68
	hg19	hg19KIndel	Indel	665,692	528,233	461,953	203,739	66,280	30.60	12.63
	hg19K	hg19KIndel	SNP	2,788,319	2,783,025	2,768,869	19,448	14,156	0.70	0.50
	hg19K	hg19KIndel	Indel	664,663	528,233	470,655	194,009	57,578	29.19	10.97

ISSN: 1471-2164