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Table S1. Mean Number of Indels and Snvs by Functional Classifications

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Table S1. Mean Number of Indels and Snvs by Functional Classifications Table S1. Mean Number of Indels and SNVs by Functional Classifications. GAIIx, 1 run GAIIx, 2 runs HiSeq 36 Mb HiSeq 36 Mb GAIIx & HiSeq, 2 runs (n=8) 50 Mb (n=19) 36 Mb (n=3) (n=10) INDELS Filtered, on-target (FOT) variants 1,069 1,202 1,260 2,276 FOT variants passed Quality Filters 1,051 1,192 1,249 2,265 Frameshift 71 76 83 210 Coding 69 78 81 102 Splice-3' 5.1 7.4 7.5 13 Splice-5' 5 5.4 5.6 8.7 UTR-3' 42.5 50.9 54.1 90.5 UTR-5' 18.5 20.3 22.5 36.8 Near-gene-3' 1.4 1.7 1.2 10.5 Near-gene-5' 4.5 4.8 4.4 18.9 Intergenic 6 6.8 6.5 141.2 Intron 846 952 995 1,644 SNVs Total # of SNPs 2,394,617 4,679,679 3,343,458 4,308,699 Filtered, on-target (FOT) variants 24,102 25,232 25,929 37,040 Transition/Transversion Ratio 2.9 2.8 2.8 2.7 FOT variants passed Quality Filters 22,236 23,951 25,187 35,410 Transition/Transversion Ratio 2.9 2.9 2.9 2.7 Nonsense 63.7 62.8 61.3 91.4 Stop gain 54.4 52.4 51.8 67.7 Stop loss 9.3 10.4 9.5 23.8 Splice 22 21.3 22.5 34.5 Coding-Synonymous 8,544 8,903 9,105 10,351 Missense 7,172 7,462 7,689 9,175 Other 8,301 8,783 9,052 17,512 1 Table S2. Genes with More Than One Missense Variant. Chr Gene Position (rsid) Family 146,461,211 1 NBPF12 146,461,276 (rs71238046) 4 146,466,083 179,642,515 3 2 TTN 179,666,982 (rs35683768) 15 38,753,903 15 3 SCN10A 38,770,119 7 9,361,398 14 4 USP17 9,361,582 16 140,557,779 (rs17844481) 16 5 PCDHB8 140,559,029 (rs73273688) 6 7,583,274 15 DSP 7,585,143 12 6 32,261,014 (rs7751028) C6orf10 5 32,261,653 (rs4947338) 51,152,961 11 COBL 51,203,928 15 7 117,180,174 5 CFTR 117,232,642 (rs1800103) 12 117,243,783 8 12,285,202 8 FAM86B2 12 12,287,930 69,432,667 (rs1924146) 16 9 CCDC29 69,432,706 11 126,678,112 15 126,678,148 15 10 CTBP2 126,682,499 1 126,683,197 1 2,814,356 16 SRRM2 10 2,814,874 45,214,633 45,214,648 45,214,651 17 CDC27 15 45,214,654 45,219,364 45,221,251 (rs1064545) 38,590,731 14 SIPA1L3 38,689,085 15 19 56,243,611 3 NLRP9 56,249,615 12 55,185,563 10 X FAM104B 55,185,656 (rs5003001) 8, 10, 15 2 Table S3. Private Missense Variants. Chr Position Gene rsID Change 1,267,729 TAS1R3 - LEU,PRO 1,905,557 KIAA1751 - THR,MET 7,887,262 PER3 - SER,ASN 8,926,474 ENO1 rs11544513 ASN,LYS 27,699,991 FCN3 - ARG,TRP 40,125,077 NT5C1A - ILE,VAL 46,651,169 TSPAN1 rs34463133 MET,ILE 89,658,689 GBP4 - ASP,TYR 109,535,450 WDR47,LOC100132742 - ARG,TRP 111,863,044 CHIA - GLY,ARG 119,936,419 HAO2 - VAL,PHE 146,461,211 NBPF12 - LEU,ARG 146,461,276 NBPF12 rs71238046 ALA,PRO 146,466,083 NBPF12 - HIS,TYR 146,493,279 LOC728989 - VAL,ILE 1 146,672,962 FMO5 - ARG,GLY 148,011,037 NBPF14 rs71261063 ASP,HIS 151,261,641 ZNF687 - GLU,LYS 155,295,681 RUSC1 - SER,PHE 173,503,768 SLC9A11 - GLU,ALA 175,365,805 TNR - ARG,GLN 197,111,665 ASPM - ARG,TRP 205,884,508 SLC26A9 - ALA,THR 210,948,886 KCNH1 - GLY,GLU 222,800,921 MIA3 - THR,MET 235,505,965 GGPS1 - ARG,CYS 235,658,082 B3GALNT2 - VAL,MET 235,922,671 LYST - GLU,ALA 236,966,848 MTR rs12749581 ARG,GLN 248,637,544 OR2T3 - ARG,HIS 229,986 SH3YL1 - GLN,ARG 20,251,265 LAPTM4A - PHE,CYS 26,700,309 OTOF - ARG,HIS 27,802,420 C2orf16 - ARG,THR 31,147,616 GALNT14 - PRO,ALA 47,601,029 TACSTD1 - GLN,HIS 48,722,897 CCDC128 - GLY,VAL 55,253,266 RTN4 - PRO,SER 80,529,551 CTNNA2,LRRTM1 - VAL,GLY 99,439,406 C2orf55 - PRO,SER 2 109,102,997 GCC2 - HIS,ASP 131,520,171 FAM123C - SER,THR 141,232,800 LRP1B rs72899872 ALA,THR 166,627,177 GALNT3 - ILE,VAL 179,642,515 TTN - PHE,LEU 179,666,982 TTN rs35683768 ASP,TYR 183,703,257 FRZB - SER,PHE 204,000,845 NBEAL1 - PRO,LEU 220,493,935 SLC4A3 - ARG,GLN 242,501,804 BOK - VAL,MET 13,896,228 WNT7A - THR,ILE 38,753,903 SCN10A - SER,THR 38,770,119 SCN10A - GLU,LYS 42,234,663 TRAK1 - SER,LEU 3 46,414,573 CCR5 rs1800940 ARG,SER 47,448,214 PTPN23 - GLU,LYS 48,638,440 UQCRC1 - GLY,SER 3 49,083,866 QRICH1 - ILE,VAL 50,005,373 RBM6 - PRO,LEU 50,334,462 HYAL3,NAT6 - ARG,TRP 75,713,555 FRG2C rs35781983 ASP,ASN 75,781,243 LOC401074,ZNF717 rs62250085 ILE,VAL 119,886,502 GPR156 - ALA,SER 121,212,545 POLQ - ARG,CYS 183,580,580 PARL - TRP,ARG 185,198,112 MAP3K13 - ASP,GLY 186,331,094 AHSG - GLY,GLU 187,003,786 MASP1 - VAL,MET 187,446,313 BCL6,LOC100131635 - ARG,CYS 197,665,522 IQCG - ARG,TRP 436,848 ZNF721 - LYS,GLU 3,443,769 HGFAC - PRO,LEU 9,361,398 USP17 - GLN,HIS 9,361,582 USP17 - SER,THR 9,405,199 LOC100133128 - ILE,LEU 4 56,820,418 CEP135 - THR,ILE 57,204,798 AASDH - THR,ALA 69,811,110 UGT2A3 rs62641705 TRP,GLY 100,130,075 ADH6 - GLY,VAL 104,030,143 CENPE - LYS,GLN 123,107,254 KIAA1109 - ARG,HIS 5,306,762 ADAMTS16 - PRO,LEU 14,487,587 TRIO - ILE,VAL 23,527,430 PRDM9 - GLU,LYS 32,088,968 PDZD2 - ILE,ARG 33,984,379 SLC45A2 - PRO,SER 34,945,012 DNAJC21 - VAL,MET 56,189,413 MAP3K1 - ARG,GLN 64,050,147 SFRS12IP1 - GLY,ALA 5 71,756,519 ZNF366 - VAL,PHE 111,071,162 C5orf13 - PHE,LEU 112,399,751 MCC - GLY,ARG 140,531,060 PCDHB6 - ASP,ASN 140,557,779 PCDHB8 rs17844481 LEU,PRO 140,559,029 PCDHB8 rs73273688 GLY,ARG 140,764,394 PCDHGA1/2/3/4/5/6/7 - VAL,GLY 145,483,756 PLAC8L1 - ARG,LYS 7,583,274 DSP - GLN,GLU 7,585,143 DSP - GLY,SER 10,529,589 GCNT2 - ASN,ASP 29,429,934 OR2H1 - TYR,HIS 31,595,698 BAT2 - ARG,TRP 32,261,014 C6orf10 rs7751028 GLY,VAL 32,261,653 C6orf10 rs4947338 LEU,TRP 32,548,544 HLA-DRB1 - ILE,LEU 36,931,208 PI16 - PRO,SER 42,713,480 TBCC - ARG,GLN 43,306,461 ZNF318 - LYS,GLU 6 70,981,360 - VAL,ILE COL9A1 74,533,259 CD109 - ARG,CYS 75,814,950 COL12A1 rs34369939 VAL,ALA 87,966,976 ZNF292 - VAL,ALA 89,975,446 GABRR2 - ARG,CYS 90,368,355 MDN1 - PRO,SER 107,420,474 KIAA1553 - PHE,VAL 132,892,017 TAAR6 - CYS,TYR 137,330,503 IL20RA - SER,TYR 137,476,104 IL22RA2 - THR,MET 4 144,750,725 UTRN - VAL,ILE 48,005,000 HUS1 - LEU,PHE 51,152,961 COBL - ARG,GLN 51,203,928 COBL - SER,LEU 77,522,948 PHTF2 - ILE,MET 87,060,844 ABCB4 rs45575636 ARG,GLN 88,965,553 ZNF804B - THR,ILE 98,995,517 PDAP1 - GLU,ALA 99,032,529 PTCD1 rs35556439 ARG,TRP 100,685,280 MUC17 - PRO,LEU 102,120,834 LOC100132214 - SER,PRO 103,835,602 ORC5L - ASP,GLY 7 107,596,043 LAMB1 - ILE,THR 107,684,224 LAMB4 - ILE,VAL 117,180,174 CFTR - ARG,GLN 117,232,642 CFTR rs1800103 ILE,MET 117,243,783 CFTR - MET,THR 117,879,968 ANKRD7 - TYR,HIS 122,338,071 CADPS2,RNF133 - LEU,PRO 124,475,422 POT1 - SER,ARG 129,691,124 ZC3HC1 - THR,ASN 138,851,618 TTC26 rs13225917 ASP,ASN 142,638,473 KEL - ASP,TYR 150,935,385 CSGlcA-T - PRO,LEU 7,808,219 LOC100132396 rs2740676 ILE,LEU 12,285,202 FAM86B2 - ASN,HIS 12,287,930 FAM86B2 - LYS,GLU 28,196,930 PNOC,LOC100129848 - ARG,GLN 37,734,870 RAB11FIP1 - ALA,THR 8 38,265,755 LETM2 - THR,MET 38,374,010 FLJ43582 - HIS,GLN 87,549,792 CPNE3 - ASP,VAL 114,449,045 CSMD3 - GLU,ASP 145,659,016 NFKBIL2 - SER,GLY 19,126,117 ADFP - PRO,LEU 27,548,576 C9orf72 - ILE,THR 32,550,896 TOPORS rs61758066 SER,TRP 35,043,871 C9orf131 - GLU,ASP 39,109,199 CNTNAP3 - GLU,LYS 68,728,863 LOC100132352 - ARG,GLY 9 69,423,521 ANKRD20A4 - ILE,THR 69,432,667 CCDC29 rs1924146 MET,LYS 69,432,706 CCDC29 - GLY,GLU 125,486,365 OR1L4 - LEU,PHE 126,133,160 CRB2 - ARG,TRP 130,914,562 LCN2 - ILE,MET 140,417,276 PNPLA7 - ARG,CYS 4,879,748 AKR1CL2 - LEU,TRP 6,268,177 PFKFB3 - PRO,LEU 29,762,841 SVIL - ARG,TRP 43,326,380 BMS1 - ARG,TRP 51,620,361 TIMM23 - SER,CYS 10 72,358,591 PRF1 - TYR,HIS 85,991,775 LRIT1 - GLU,LYS 90,499,808 LIPK - MET,ARG 95,791,147 PLCE1 - HIS,PRO 96,093,938 NOC3L - HIS,ARG 100,995,498 HPSE2 - CYS,TYR 116,045,781 VWA2 - ARG,TRP 126,682,499 CTBP2 - LYS,ARG 126,683,197 CTBP2 - ILE,MET 5 126,799,611 CTBP2,LOC100132971 - LYS,GLU 134,942,110 GPR123 - ALA,THR 551,708 LRRC56 - THR,MET 702,962 TMEM80 - THR,PRO 799,542 LRDD - ARG,HIS 1,092,760 MUC2 - THR,PRO 1,213,556 MUC5AC rs74046249 ARG,LYS 4,967,540 OR51A4 - ARG,HIS 6,048,408 OR56A1 - CYS,PHE 10,800,639 CTR9 - ASP,VAL 18,568,501 UEVLD - ASP,GLY 32,118,694 RCN1 - ILE,VAL 32,674,734 CCDC73 - ARG,TRP 46,917,560 LRP4 - THR,MET 11 49,598,257 LOC440040 rs7101891 VAL,LEU 55,658,893 SPRYD5 rs34250328 CYS,ARG 62,458,312 BSCL2 - PRO,LEU 65,305,564 SCYL1 - ARG,TRP 66,834,232 RHOD - ARG,TRP 68,478,487 MTL5 - CYS,ARG 74,547,278 RNF169 - GLU,LYS 74,914,359 SLCO2B1 - MET,ILE 89,028,453 TYR - LYS,ASN 92,714,766 MTNR1B - GLY,ASP 104,900,536 CASP1 - ARG,TRP 124,007,900 LOH11CR2A rs73015627 PRO,SER 3,805,977 EFCAB4B - ASP,GLU 3,923,203 PARP11 - GLY,ARG 6,127,833 VWF rs1800386 TYR,CYS 11,506,471 PRB1 - LYS,ARG 21,615,735 PYROXD1 - ASP,GLY 21,624,546 RECQL rs6499 ASP,HIS 12 45,059,357 NELL2 - ARG,CYS 48,886,771 C12orf54 - ARG,GLY 102,046,985 MYBPC1 - GLY,ARG 108,136,105 PRDM4 - LEU,SER 124,824,869 NCOR2 rs61755988 THR,MET 133,365,741 GOLGA3 - ARG,TRP 33,017,503 N4BP2L2 - GLY,ARG 13 113,825,992 PROZ - GLU,VAL 20,528,309 OR4L1 - GLY,CYS 20,585,689 OR4K17 - GLU,LYS 20,711,179 OR11H4 - ALA,PRO 24,607,804 PSME1 - ARG,LYS 14 36,017,741 GARNL1 - HIS,ARG 55,604,883 LGALS3 - GLY,ARG 70,175,690 KIAA0247 rs45544938 VAL,GLY 93,275,714 GOLGA5 rs34515753 ARG,GLN 96,781,723 ATG2B - LYS,GLU 24,922,053 C15orf2 rs34629208 ASP,TYR 48,713,794 FBN1 - ARG,TRP 57,820,876 CGNL1 - ARG,TRP 15 69,732,770 KIF23 - ARG,TRP 75,798,027 PTPN9 - PHE,LEU 86,283,483 AKAP13 - GLU,LYS 90,168,736 C15orf42 - THR,MET 101,718,677 CHSY1 - MET,THR 2,814,356 SRRM2,LOC100132779 - GLU,GLY 2,814,874 SRRM2,LOC100132779 - ASP,HIS 16 21,245,101 ANKS4B - GLU,GLN 22,826,241 HS3ST2 - SER,PRO 6 23,701,251 PLK1 - ARG,HIS 30,364,505 CD2BP2 - MET,ILE 4,098,747 ANKFY1 - ILE,VAL 4,540,514 ALOX15 - GLY,ARG 7,762,859 CYB5D1 - LEU,PHE 7,839,694 CNTROB rs61747003 ARG,LEU 7,910,817 GUCY2D rs61749682 LEU,PHE 7,948,239 ALOX15B - LEU,PHE 17,127,274 FLCN - ARG,TRP 18,653,403 FBXW10 - ASP,ASN 19,684,338 ULK2 - LYS,GLU 20,799,166 MGC87631 - ASN,LYS 27,023,927 SUPT6H - MET,LEU 27,182,060 ERAL1 - ALA,GLY 31,351,014 ACCN1 rs16967895 ASP,GLY
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