Representativeness of variation benchmark datasets

BMC Bioinformatics

Table 3 Analysis of the chromosomal distribution of variants in dataset DS1

Chromosome	no. of genes	CDS length	no. of observed variants	no. of expected variants (no. of genes)	no. of expected variants (CDS length)	p-value^a (no of genes)	p-value^a (CDS length)
1	2037	3,483,903	45,856	45,915	45,339	0.773155	0.010565
2	1238	2,517,642	31,391	27,905	32,765	< 10⁻⁴	< 10–4
3	1071	1,965,098	24,735	24,141	25,574	< 10⁻⁴	< 10–4
4	745	1,365,661	16,936	16,793	17,773	0.260634	< 10–4
5	882	1,601,648	19,148	19,881	20,844	< 10⁻⁴	< 10–4
6	1035	1,735,760	22,495	23,330	22,589	< 10^− 4	0.523159
7	901	1,609,177	21,764	20,309	20,942	< 10⁻⁴	< 10–4
8	668	1,135,640	16,239	15,057	14,779	< 10⁻⁴	< 10–4
9	770	1,382,150	19,117	17,356	17,987	< 10^− 4	< 10–4
10	727	1,322,286	17,489	16,387	17,208	< 10⁻⁴	0.0292
11	1278	2,005,315	28,704	28,807	26,097	0.532354	< 10–4
12	1033	1,776,908	20,797	23,284	23,125	< 10⁻⁴	< 10–4
13	324	634,435	7401	7303	8257	0.247573	< 10–4
14	614	1,079,560	13,972	13,840	14,049	0.254342	0.511939
15	589	1,189,858	14,846	13,276	15,485	< 10⁻⁴	< 10–4
16	858	1,451,775	22,351	19,340	18,893	< 10⁻⁴	< 10–4
17	1184	1,971,211	26,518	26,688	25,653	0.284589	< 10–4
18	268	534,152	6644	6041	6951	< 10⁻⁴	0.000187
19	1467	2,277,812	34,032	33,067	29,643	< 10⁻⁴	< 10–4
20	540	811,690	11,340	12,172	10,563	< 10⁻⁴	< 10–4
21	233	342,226	5194	5252	4454	0.424789	< 10–4
22	439	712,404	10,412	9895	9271	< 10⁻⁴	< 10–4
X	840	1,296,174	8557	18,934	16,868	< 10⁻⁴	< 10–4
Y	45	67,500	51	1014	878	< 10⁻⁴	0.010565

ISSN: 1471-2105