Assessing structural variation in a personal genome—towards a human reference diploid genome

English, Adam C; Salerno, William J; Hampton, Oliver A; Gonzaga-Jauregui, Claudia; Ambreth, Shruthi; Ritter, Deborah I; Beck, Christine R; Davis, Caleb F; Dahdouli, Mahmoud; Ma, Singer; Carroll, Andrew; Veeraraghavan, Narayanan; Bruestle, Jeremy; Drees, Becky; Hastie, Alex; Lam, Ernest T; White, Simon; Mishra, Pamela; Wang, Min; Han, Yi; Zhang, Feng; Stankiewicz, Pawel; Wheeler, David A; Reid, Jeffrey G; Muzny, Donna M; Rogers, Jeffrey; Sabo, Aniko; Worley, Kim C; Lupski, James R; Boerwinkle, Eric; Gibbs, Richard A

doi:10.1186/s12864-015-1479-3

BMC Genomics

Table 3 Exonic SVs with assembly support absent from DGV

From: Assessing structural variation in a personal genome—towards a human reference diploid genome

Gene	Chr	Start	End	Type	Source	Flag
ASTN1	1	177,131,105	177,139,508	INS	ARR,ILL,PAC	7
C16orf96	16	4,619,222	4,629,905	INS	ARR,ILL,PAC	7
DOCK3	3	50,879,021	50,879,201	INS	ILL,PAC	7
PCNXL4	14	60,575,443	60,575,546	INS	ILL,PAC	7
PKD1L3	16	72,030,321	72,032,511	INS	ILL,PAC	7
TBC1D3G	17	34,805,579	34,815,084	DEL	ILL,PAC	7
MAGEA11	X	148,735,694	148,830,894	MIS	ILL,NEX	6
METTL21C	13	103,345,467	103,348,148	INS	ILL,NEX	6
RAP1GDS1	4	99,179,171	99,184,420	DEL	ARR	5
ZNF826P	19	20,504,301	20,595,300	DEL	ILL	5
ASTN1	1	177,131,101	177,139,495	MIS	ILL	5
C20orf96	20	258,785	260,245	DEL	ARR	5
CSMD3	8	113,234,275	113,239,237	DEL	NEX	5
GMCL1	2	70,066,401	70,071,781	MIS	NEX	5
HLA-DRB1	6	32,547,848	32,548,158	DEL	ILL	5
MLF1IP	4	185,651,743	185,652,393	INS	ILL	5
MTO1	6	74,203,747	74,216,637	MIS	ILL	5
MUC2	11	1,092,829	1,093,579	INS	ILL	5
OR4C6	11	55,431,550	55,457,289	INS	ILL	5
PDE4DIP	1	144,954,098	144,960,871	MIS	ILL	5
RAB11FIP3	16	544,841	547,158	INS	NEX	5
AP2A2	11	915,248	928,463	INS	ARR	4
TPSB2	16	1,274,089	1,288,819	INS	ARR	4
TPSG1	16	1,274,089	1,288,819	INS	ARR	4
ALDH16A1	19	49,966,580	49,968,737	INS	NEX	4
ASMTL	X	1,550,501	1,572,400	INS	ILL	4
C14orf39	14	60,913,981	60,941,067	MIS	ILL	4
CCL24	7	75,438,336	75,451,936	INS	ILL	4
CD99	X	2,651,401	2,699,500	INS	ILL	4
CNTNAP3B	9	43,844,101	43,866,100	INS	ILL	4
CTNNA2	2	80,769,022	80,780,356	MIS	ILL	4
DEFA1	8	6,833,701	6,844,000	DEL	ILL	4
DSPP	4	88,536,463	88,536,667	INS	ILL	4
ENPP7	17	77,699,565	77,726,581	MIS	ILL	4
EXOC6B	2	72,688,192	72,697,903	MIS	ILL	4
FAM186A	12	50,745,742	50,745,861	INS	PAC	4
FOXO6	1	41,847,826	41,847,932	INS	PAC	4
FRK	6	116,274,618	116,307,096	MIS	ILL	4
HERC2	15	28,547,301	28,566,700	INS	ILL	4
HSD17B3	9	99,057,917	99,063,709	MIS	ILL	4
IFNAR1	21	34,694,683	34,701,442	MIS	NEX	4
IGHV4-61	14	107,087,259	107,099,190	INS	ILL	4
IL28A	19	39,730,613	39,762,849	MIS	NEX	4
IL28B	19	39,730,613	39,762,849	MIS	NEX	4
IL3RA	X	1,494,601	1,510,800	INS	ILL	4
KIAA1671	22	25,441,077	25,467,572	INS	ILL	4
KRT37	17	39,579,211	39,595,476	MIS	ILL	4
KRT38	17	39,579,211	39,595,476	MIS	ILL	4
KRTAP4-7	17	39,240,740	39,240,840	INS	PAC	4
KRTAP5-4	11	1,642,915	1,643,128	INS	PAC	4
MATR3	5	138,652,720	138,666,146	INS	ARR	4
NBPF15	1	148,571,852	148,591,725	INS	ARR	4
OR2A7	7	143,945,501	143,956,800	INS	ILL	4
OR2G6	1	248,682,789	248,702,341	MIS	NEX	4
OR4C3	11	48,340,701	48,347,600	INS	ILL	4
OR4C6	11	55,431,551	55,445,867	INS	PAC	4
OR8U1	11	56,143,129	56,143,999	INS	PAC	4
PLXNB2	22	50,723,862	50,724,455	DEL	ILL	4
PPP2R3B	X	290,201	300,100	INS	ILL	4
PPP2R3B	X	327,401	344,700	INS	ILL	4
PRIM2	6	57,494,250	57,507,908	INS	ILL	4
RFC1	4	39,350,151	39,353,407	INS	NEX	4
RGPD3	2	107,082,401	107,085,300	DEL	ILL	4
RRBP1	20	17,639,769	17,639,981	INS	PAC	4
SAMD1	19	14,200,852	14,200,953	INS	PAC	4
SHOX	X	598,001	628,300	INS	ILL	4
SLC25A6	X	1,494,601	1,510,800	INS	ILL	4
SMC1B	22	45,745,435	45,746,440	INS	ILL	4
TMEFF2	2	192,818,912	192,840,053	MIS	ILL	4
UTS2D	3	190,999,450	191,019,577	INS	ILL	4
XG	X	2,651,401	2,699,500	INS	ILL	4
ZNF208	19	22,156,807	22,156,912	DEL	PAC	4
ZNF253	19	19,990,342	20,005,317	MIS	ILL	4
ZNF346	5	176,462,777	176,474,191	INS	ILL	4
ZNF519	18	14,105,158	14,105,265	DEL	PAC	4

Genomic location, SV type, Parliament bitflag, and supporting data types are provided for the 75 HS1011 SVs overlapping an exon but not matching a DGV event.

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ISSN: 1471-2164

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