Table 3 Variant statistics for both genome builds

From: Alternate-locus aware variant calling in whole genome sequencing

	GRCh37				GRCh38
Chromosome	All	Common	Rare	Phred	All	Common	Rare	Phred
1	344158	299500	44659	503.42	359530	291704	67825	473.83
2	354113	247585	106528	506.54	361469	243400	118069	492.91
3	295447	268021	27426	503.76	301985	263993	37993	492.99
4	319988	290080	29908	515.41	324134	285405	38729	507.33
5	266077	235462	30615	498.58	272482	231747	40734	485.57
6	280789	252705	28084	495.02	279132	246545	32588	487.11
7	249980	220543	29437	488.95	257917	216669	41248	475.69
8	229332	204823	24509	499.70	229541	200845	28696	490.15
9	192615	162202	30413	475.09	200034	159119	40916	466.46
10	217957	194385	23572	508.74	229352	190658	38694	494.18
11	219134	197412	21722	522.84	228324	194132	34192	498.04
12	205085	184477	20608	502.78	212789	175990	36799	483.94
13	166128	151271	14856	530.31	180521	148870	31651	494.65
14	141971	124790	17181	503.15	140443	122524	17919	495.75
15	130324	112085	18239	505.95	131389	109741	21648	493.46
16	134293	116224	18069	487.40	136799	113589	23210	473.36
17	118096	102300	15796	479.64	130637	99074	31563	452.99
18	124509	111958	12552	516.80	132628	110349	22279	485.89
19	98104	84416	13688	456.51	99625	82875	16750	455.35
20	90490	79709	10781	486.09	112562	78562	33999	475.40
21	69511	55211	14300	525.23	73027	53052	19975	513.27
22	59660	50242	9418	455.99	71112	48961	22151	445.27
Total	4307761				4465432

The mean counts of autosomal variants and the median Phred scores per chromosome are shown for GRCh37 and GRCh38.
Columns: All: all detected variants; Common: listed in dbSNP common_all_*; Rare: variants that are not common.
The mean variant counts for chromosome X were 127,914 (GRCh37) and 132,177 (GRCh38). For chromosome Y, the mean counts could not be estimated since gender information was not available for all of the 121 in-house genomes. Both genome releases include the identical mitochondrial reference (NC_012920.1) with 27 variants

Back to article page

ISSN: 1756-994X

Contact us

Submission enquiries: editorial@genomemedicine.com
General enquiries: info@biomedcentral.com