Next-generation sequencing for D47N mutation in Cx50 analysis associated with autosomal dominant congenital cataract in a six-generation Chinese family

Shen, Chao; Wang, Jingbing; Wu, Xiaotang; Wang, Fuchao; Liu, Yang; Guo, Xiaoying; Zhang, Lina; Cao, Yanfei; Cao, Xiuhua; Ma, Hongxing

doi:10.1186/s12886-017-0476-5

Table 2 Variations identified by whole exome sequencing

From: Next-generation sequencing for D47N mutation in Cx50 analysis associated with autosomal dominant congenital cataract in a six-generation Chinese family

Mutation type	III12	IV11	IV28	IV30	IV73	V9	V27	VI3	VI9	VI15	IV40
Indel analysis
Total	15,930	15,690	15,489	13,623	15,448	15,678	18,613	14,028	14,873	14,520	15,657
1000genome and dbsnp	6813	6707	6678	6153	6663	6561	8340	6123	6324	6375	6586
1000genome specific	151	134	128	132	131	143	170	154	129	128	122
dbSNP specific	4846	4570	4462	3853	4544	4448	5594	4036	4406	4324	4559
dbSNP rate	73.19%	71.87%	71.92%	73.45%	72.55%	70.22%	74.86%	72.42%	72.14%	73.68%	71.18%
Novel	4120	4279	4221	3485	4110	4526	4509	3715	4014	3693	4390
Homozygous	4857	4935	4803	4405	4612	4448	3181	4304	4534	4601	4686
Heterozygous	11,073	10,755	10,686	9218	10,836	11,230	15,432	9724	10,339	9919	10,971
Frameshift	374	413	394	394	406	458	423	392	417	387	397
Non-frameshift Insertion	158	180	189	153	181	208	195	173	189	164	169
Non-frameshift Deletion	61	62	63	67	66	81	83	68	66	72	60
Non-frameshift codon substitution plus Insertion	61	77	61	58	73	80	88	70	75	55	84
Non-frameshift codon substitution plus Deletion	28	28	35	25	33	34	30	38	25	23	26
Stopgain	4	14	10	4	9	5	7	9	9	10	12
Stoploss	1	1	0	0	1	2	2	1	1	1	1
Startloss	0	1	0	0	2	0	2	1	0	1	1
Exonic	689	777	754	702	772	869	832	754	782	715	751
Splicing	62	58	57	59	62	60	60	63	61	57	66
NcRNA	238	229	240	235	233	249	259	239	223	222	248
UTR5	178	194	188	180	186	198	216	174	172	174	203
UTR3	1530	1510	1427	1276	1498	1471	1797	1372	1414	1382	1519
Intronic	11,915	11,636	11,562	10,061	11,403	11,572	13,936	10,245	10,997	10,788	11,579
Upstream	283	280	307	266	304	293	338	242	279	239	284
Downstream	733	710	683	603	740	708	846	663	682	688	738
Intergenic	302	296	271	241	250	258	329	276	263	255	269
SNP analysis
Total	134,311	134,225	136,378	129,878	134,039	133,761	166,869	127,698	130,216	131,224	134,002
1000genome and dbsnp	121,404	120,889	122,334	116,489	120,656	119,805	152,022	114,903	117,222	117,467	119,890
1000genome specific	443	456	451	450	466	500	503	473	473	443	436
dbSNP specific	4979	5030	5142	4963	5008	5188	5533	4875	5051	5034	5008
dbSNP rate	94.10%	93.81%	93.47%	93.51%	93.75%	93.45%	94.42%	93.80%	93.90%	93.35%	93.21%
Novel	7485	7850	8451	7976	7909	8268	8811	7447	7470	8280	8668
Homozygous	51,982	53,569	52,947	51,462	51,793	50,013	32,944	48,638	50,529	51,424	51,815
Heterozygous	82,329	80,656	83,431	78,416	82,246	83,748	133,925	79,060	79,687	79,800	82,187
Synonymous	11,043	11,075	11,209	10,961	10,967	11,123	14,116	11,169	11,048	11,104	11,215
Missense	10,750	10,857	10,991	10,820	10,768	11,029	13,713	10,878	10,892	10,768	10,992
Stopgain	100	113	117	110	102	109	139	113	111	117	113
Stoploss	30	33	31	30	28	35	34	33	31	35	27
Startgain	506	509	496	468	524	491	639	466	487	495	503
Startloss	30	29	26	27	30	30	36	24	29	30	32
Exonic	21,979	22,126	22,390	21,970	21,916	22,346	28,067	22,241	22,131	22,075	22,402
Splicing	159	162	166	149	150	156	191	168	157	157	158
NcRNA	3252	3279	3410	3233	3381	3329	3809	3283	3281	3245	3284
UTR5	1981	2028	2080	1993	2015	2096	2498	1908	1948	1968	2061
UTR3	7707	7707	7821	7485	7825	7652	9778	7461	7527	7610	7820
Intronic	89,844	89,674	91,108	86,065	89,445	88,742	111,479	83,963	86,127	87,172	89,093
Upstream	2248	2299	2339	2195	2262	2344	2743	2040	2170	2152	2237
Downstream	4596	4483	4540	4325	4523	4471	5408	4202	4364	4429	4516
Intergenic	2545	2467	2524	2463	2522	2625	2896	2432	2511	2416	2431
SIFT	1859	1905	1934	1819	1833	1939	2556	1918	1866	1892	1904

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ISSN: 1471-2415

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