Characterization and identification of hidden rare variants in the human genome

BMC Genomics

Table 2 GENCODE and ENCODE annotations of all the RRA loci for GRCh37 and GRCh38

Type	Total variants (GRCh37)	Class A	Class B	Class C	Total variants (GRCh38)	Class A	Class B	Class C
Total SNVs	85111	17944	60714	6453	77274	11827	59055	6392
Intergenic	40321	8004	29053	3264	36774	5465	28072	3237
Gencode	44790	9940	31661	3189	40500	6362	30983	3155
Functional	580	167	373	40	402	31	335	36
Pseudogenes	734	135	518	81	633	68	487	78
Non coding RNA	8628	2040	5965	623	7673	1229	5828	616
Encode Elements	20438	4723	14138	1577	18458	3098	13811	1549
Total Insertions	6700	1870	4616	214	17	5	10	2
Intergenic	2912	751	2052	109	7	1	5	1
Gencode	3788	1119	2564	105	10	4	5	1
Functional	56	23	31	2	1	0	1	0
Pseudogenes	61	14	44	3	1	0	0	1
Non coding RNA	744	243	477	24	4	2	2	0
Encode Elements	1744	569	1122	53	4	1	3	0
Total Deletions	4462	1206	3095	161	3703	689	2857	157
Intergenic	1869	504	1298	67	1523	290	1168	65
Gencode	2593	702	1797	94	2180	399	1689	92
Functional	24	8	15	1	9	1	7	1
Pseudogenes	30	10	20	0	19	17	2	0
Non coding RNA	486	137	333	16	392	64	312	16
Encode Elements	1023	304	682	37	823	154	633	36

Columns report the total number of variants (Total Variants), the number of variants that belong to classes A, B, and C for all RRA SNVs and InDels in GRCh37 and GRCh38. Rows report the annotation features at which each RRA has been annotated.

ISSN: 1471-2164