Copy Number Variation detection from 1000 Genomes project exon capture sequencing data

Wu, Jiantao; Grzeda, Krzysztof R; Stewart, Chip; Grubert, Fabian; Urban, Alexander E; Snyder, Michael P; Marth, Gabor T

doi:10.1186/1471-2105-13-305

BMC Bioinformatics

Table 5 Gene deletion calls in the BI dataset

From: Copy Number Variation detection from 1000 Genomes project exon capture sequencing data

Population	Sample	Gene name	Gene function	Chr	Start [bp]	End [bp]	Posterior probability	RD _observed	RD _expected
CHD	NA18695	TPM3	tropomyosin 3	1	152396739	152422219	1.000	166	337
JPT	NA19066	TPM3	tropomyosin 3	1	152396739	152422219	1.000	169	288
CHD	NA18687	RPL27A	ribosomal protein L27a	11	8661325	8663929	1.000	93	182
JPT	NA18983	POU5F1	POU class 5 homeobox 1	6	31240357	31241803	1.000	122	256
JPT	NA19066	POU5F1	POU class 5 homeobox 1	6	31240357	31241803	1.000	166	318
JPT	NA19066	RPL27A	ribosomal protein L27a	11	8661325	8663929	1.000	106	203
CHD	NA18687	TPM3	tropomyosin 3	1	152396739	152422219	1.000	155	258
CHD	NA18687	POU5F1	POU class 5 homeobox 1	6	31240357	31241803	1.000	156	285
JPT	NA19054	TPM3	tropomyosin 3	1	152396739	152422219	1.000	135	230
CHD	NA18695	POU5F1	POU class 5 homeobox 1	6	31240357	31241803	1.000	194	371
JPT	NA18960	SETD8	SET domain containing (lysine methyltransferase) 8	12	122441130	122455574	1.000	221	347
CHD	NA18164	RPL27A	ribosomal protein L27a	11	8661325	8663929	1.000	129	223
JPT	NA19054	POU5F1	POU class 5 homeobox 1	6	31240357	31241803	1.000	130	254
CHD	NA18695	SETD8	SET domain containing (lysine methyltransferase) 8	12	122441130	122455574	1.000	142	309
CHD	NA18695	RPL27A	ribosomal protein L27a	11	8661325	8663929	1.000	128	238
CHD	NA18695	AKR1B1	aldo-keto reductase family 1, member B1 (aldose reductase)	7	133778020	133787045	1.000	310	554
CHD	NA18164	HAX1	HCLS1 associated protein X-1	1	152512874	152514801	1.000	214	339
CHD	NA18687	SETD8	SET domain containing (lysine methyltransferase) 8	12	122441130	122455574	1.000	125	237
JPT	NA19054	HFE	hemochromatosis	6	26201326	26202433	1.000	56	122
JPT	NA18983	RPL27A	ribosomal protein L27a	11	8661325	8663929	0.990	95	164
JPT	NA18983	TPM3	tropomyosin 3	1	152396739	152422219	0.990	147	232
JPT	NA19561	TRIM55	tripartite motif-containing 55	8	67202058	67209944	0.990	119	193
CHD	NA18687	RBMS1	RNA binding motif, single stranded interacting protein 1	2	160840394	160932124	0.990	334	575
CHB	NA18757	CRIPAK	cysteine-rich PAK1 inhibitor	4	1378300	1379640	0.990	327	669
JPT	NA19054	PSAT1	phosphoserine aminotransferase 1	9	80109471	80113319	0.980	140	253
JPT	NA19066	PSAT1	phosphoserine aminotransferase 1	9	80109471	80113319	0.980	190	317
CHD	NA18164	TPM3	tropomyosin 3	1	152396739	152422219	0.980	209	317
JPT	NA19568	OR8A1	olfactory receptor, family 8, subfamily A, member 1	11	123945175	123946141	0.980	471	764
JPT	NA19066	RAN	RAN, member RAS oncogene family	12	129923334	129926424	0.980	229	462
CHD	NA18695	KLHL12	kelch-like 12	1	201128284	201160913	0.970	767	1358
JPT	NA19066	SETD8	SET domain containing (lysine methyltransferase) 8	12	122441130	122455574	0.970	154	265
JPT	NA19066	RPS15A	ribosomal protein S15a	16	18706886	18707936	0.960	83	161
CHD	NA18695	RPS15A	ribosomal protein S15a	16	18706886	18707936	0.960	88	188
CHD	NA18687	KLHL12	kelch-like 12	1	201128284	201160913	0.960	621	1041
JPT	NA18983	SETD8	SET domain containing (lysine methyltransferase) 8	12	122441130	122455574	0.960	120	213
JPT	NA18983	DCTN5	dynactin 5 (p25)	16	23560365	23585966	0.960	177	298
JPT	NA18983	EIF2B5	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82 kDa	3	185500333	185509372	0.940	856	1482
CHD	NA18687	ARG2	arginase, type II	14	67187855	67187951	0.940	28	62
CHD	NA18695	PSAT1	phosphoserine aminotransferase 1	9	80109471	80113319	0.930	221	371
CHD	NA18695	RBMS1	RNA binding motif, single stranded interacting protein 1	2	160840394	160932124	0.900	442	750
JPT	NA19561	OR8A1	olfactory receptor, family 8, subfamily A, member 1	11	123945175	123946141	0.890	254	466
YRI	NA19247	TIMM8B	translocase of inner mitochondrial membrane 8 homolog B (yeast)	11	111461229	111462657	0.880	40	89
CHD	NA18164	POU5F1	POU class 5 homeobox 1	6	31240357	31241803	0.850	226	349
CHD	NA18164	KLHL12	kelch-like 12 (Drosophila)	1	201128284	201160913	0.800	803	1276
CHD	NA18164	SETD8	SET domain containing (lysine methyltransferase) 8	12	122441130	122455574	0.790	181	291
CHD	NA18687	RPS15A	ribosomal protein S15a	16	18706886	18707936	0.790	81	144
JPT	NA19066	EIF2B5	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82 kDa	3	185500333	185509372	0.780	1137	1840
JPT	NA19568	GABARAPL2	GABA(A) receptor-associated protein-like 2	1	157676173	157676631	0.760	254	476
JPT	NA19560	OR8A1	olfactory receptor, family 8, subfamily A, member 1	11	123945175	123946141	0.750	614	1119
JPT	NA19058	RPL27	ribosomal protein L27	17	38404294	38408463	0.730	356	518
CHD	NA18699	SDPR	serum deprivation response	2	192408894	192419896	0.720	524	1033
JPT	NA18983	SPRR2G	small proline-rich protein 2 G	1	151388989	151389210	0.670	81	147
JPT	NA19066	SPRR2G	small proline-rich protein 2 G	1	151388989	151389210	0.670	105	182
JPT	NA19066	RBMS1	RNA binding motif, single stranded interacting protein 1	2	160840394	160932124	0.670	404	642
JPT	NA19054	EIF2B5	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82 kDa	3	185500333	185509372	0.670	869	1470
CHD	NA18695	RAN	RAN, member RAS oncogene family	12	129923334	129926424	0.660	290	539

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ISSN: 1471-2105

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