Table 2 Sequence depth and proportion of each allele around the 3′ part of exon 2 region in HLA-A gene

From: Comparison of exome-based HLA class I genotyping tools: identification of platform-specific genotyping errors

				A25:01/A25:01				A25:01/A03:01				A03:01/A03:01
				Depth				Depth				Depth
No	Position in HLA-A ^a		Chromosome location	Total	A03:01*	A25:01*	Proportion of A25:01*	Total	A03:01*	A25:01*	Proportion of A25:01*	Total	A03:01*	A25:01*	Proportion of A25:01*
Mapped to hg19 reference (A03:01)*
1	exon 2	184	29 910 716	31	0	31	100%	34	20	14	41%	69	69	0	0%
2	exon 2	186	29 910 717	31	0	31	100%	33	19	14	42%	59	59	0	0%
3	exon 2	188	29 910 730	30	0	30	100%	33	19	14	42%	55	55	0	0%
4	exon 2	209	29 910 742	26	0	26	100%	30	20	10	33%	63	63	0	0%
5	exon 2	226	29 910 759	1	0	1	100%	23	23	0	0%	60	60	0	0%
6	exon 2	228	29 910 761	1	0	1	100%	23	23	0	0%	60	60	0	0%
7	exon 2	229	29 910 762	1	0	1	100%	23	23	0	0%	60	60	0	0%
8	exon 2	234	29 910 767	1	0	1	100%	25	25	0	0%	60	60	0	0%
9	exon 2	238	29 910 771	1	0	1	100%	24	24	0	0%	60	60	0	0%
10	exon 2	240	29 910 773	1	0	1	100%	23	23	0	0%	60	60	0	0%
11	exon 2	241	29 910 774	1	0	1	100%	23	23	0	0%	60	60	0	0%
12	exon 2	244	29 910 777	1	0	1	100%	24	24	0	0%	60	60	0	0%
13	exon 2	246	29 910 779	1	0	1	100%	25	25	0	0%	59	59	0	0%
14	exon 2	268	29 910 801	14	0	14	100%	31	26	5	16%	60	60	0	0%
15	Intron 2	17	29 910 820	18	0	18	100%	30	22	8	27%	56	56	0	0%
16	Intron 2	31	29 910 834	21	0	21	100%	29	20	9	31%	48	48	0	0%
Mapped to modified hg19 reference (A25:01)*
1	exon 2	184	29 910 716	53	0	53	100%	37	14	23	62%	47	47	0	0%
2	exon 2	186	29 910 717	53	0	53	100%	35	12	23	66%	43	43	0	0%
3	exon 2	188	29 910 730	53	0	53	100%	36	13	23	64%	44	44	0	0%
4	exon 2	209	29 910 742	41	0	41	100%	35	12	23	66%	50	50	0	0%
5	exon 2	226	29 910 759	36	0	36	100%	29	3	26	90%	21	21	0	0%
6	exon 2	228	29 910 761	39	0	39	100%	29	3	26	90%	19	19	0	0%
7	exon 2	229	29 910 762	39	0	39	100%	29	3	26	90%	19	19	0	0%
8	exon 2	234	29 910 767	41	0	41	100%	27	3	24	89%	19	19	0	0%
9	exon 2	238	29 910 771	40	0	40	100%	27	3	24	89%	19	19	0	0%
10	exon 2	240	29 910 773	39	0	39	100%	28	3	25	89%	19	19	0	0%
11	exon 2	241	29 910 774	38	0	38	100%	28	3	25	89%	19	19	0	0%
12	exon 2	244	29 910 777	35	0	35	100%	28	3	25	89%	19	19	0	0%
13	exon 2	246	29 910 779	34	0	34	100%	29	4	25	86%	19	19	0	0%
14	exon 2	268	29 910 801	36	0	36	100%	38	14	24	63%	49	49	0	0%
15	Intron 2	17	29 910 820	29	0	29	100%	35	14	21	60%	48	48	0	0%
16	Intron 2	31	29 910 834	30	0	30	100%	34	14	20	59%	45	45	0	0%

No. 5 to 13 is corresponding to the part within the underlined sequences in red in Figure 4a.
^aThe position is corresponding to the position in Figure 4a.

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Table 2 Sequence depth and proportion of each allele around the 3′ part of exon 2 region in HLA-A gene

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