Spreadsheet: 242d52b7-71b7-4655-af4e-deeef50d416f
Sheet: Table S1 Performance data

Table [NAME] exome sequencing performance and variant count
Sample | Library typea | Library preparationb | Capture methodc | Sequence reads | Read length (bp) | Instrument | Total reads | % Reads mapped | % Mapped reads duplicates | % Reads OnTargetd | % Target bases ≥1-fold Coverage | % Target bases ≥10-fold Coverage | % Target bases ≥20-fold Coverage | Mean coverage for target bases | % Target bases with one fifth of mean coverage | Novel deleterious (and nonsynonymous) variants per individual | Novel deleterious (and nonsynonymous) variants shared by all relativese
1.1 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 75 | GAIIx | 75032300 | 93.9 | 11.43 | 76.06 | 98.87 | 94.46 | 89.15 | 106 | 88 | 34 (260) | 12 (111)
1.2 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 75 | GAIIx | 74918338 | 93.96 | 10.81 | 77.99 | 98.84 | 94.38 | 89.02 | 110.07 | 87.29 | 26 (257)
2.1 | PE | SPRIworks (200-400 bp) | Ag Exome 50 Mb | PE | 75 | GAIIx | 107992282 | 93.96 | 7.91 | 60.06 | 98.05 | 84.93 | 73.83 | 71.82 | 79.09 | 74 (352) | 21 (149)
2.2 | PE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 75 | GAIIx | 72099078 | 98.98 | 12.36 | 63.79 | 97.31 | 80.18 | 66.87 | 56.49 | 77.16 | 39 (274)
3.1 | PE | SPRIworks (200-400 bp) | NG exome array | SE | 75 | GAIIx | 47592209 | 97.1 | 57.94 | 66.48 | 99.28 | 93.75 | 82.71 | 63.54 | 90.82 | 14 (236) | 4 (108)
3.2 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | SE | 75 | GAIIx | 56988571 | 98.79 | 41.63 | 72.55 | 99.16 | 94.52 | 87.39 | 87.43 | 88.95 | 17 (263)
4.1 | SE | Manual (Gel 200-300 bp) | NG exome array | SE | 75 | GAIIx | 59105880 | 96.06 | 54.3 | 74.56 | 99.16 | 92.35 | 82.67 | 88.55 | 84.63 | 27 (262) | 0 (7)
4.2 | SE | Manual (Gel 200-300 bp) | NG exome array | SE | 75 | GAIIx | 57455413 | 95.68 | 70.4 | 68.45 | 98.87 | 92.36 | 82.94 | 81.07 | 85.84 | 24 (210)
5.1 | SE | Manual (Gel 200-300 bp) | NG exome array | SE | 75 | GAIIx | 38840503 | 95.11 | 46.18 | 69.6 | 99.37 | 91 | 77.28 | 47.09 | 91 | 15 (223) | 0 (4)
5.2 | SE | Manual (Gel 200-300 bp) | NG exome array | SE | 75 | GAIIx | 47470822 | 97.42 | 38.59 | 70.51 | 99.4 | 93.4 | 83.28 | 57.99 | 91.58 | 24 (246)
5.3 | SE | Manual (Gel 200-300 bp) | NG exome array | SE | 75 | GAIIx | 39951335 | 95.23 | 43.6 | 68.97 | 98.77 | 86.11 | 70.9 | 55.05 | 82.91 | 17 (197)
6.1 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 77589764 | 98.69 | 15.41 | 63.43 | 97.87 | 83.56 | 72.41 | 69.89 | 78.74 | 38 (298) | 7 (65)
6.2 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 85197176 | 98.67 | 16.61 | 70.84 | 97.83 | 85.84 | 76.51 | 86.08 | 78.23 | 34 (290)
7.1 | PE | SPRIworks (200-400 bp) | NG exome array | PE | 75 | GAIIx | 25248866 | 98.11 | 17.54 | 65.86 | 98.65 | 81.36 | 59.52 | 34.28 | 88.54 | 23 (214) | 1 (29)
7.2 | PE | SPRIworks (200-400 bp) | NG exome array | PE | 75 | GAIIx | 60353464 | 98.58 | 48.37 | 71.38 | 99.47 | 96.09 | 87.65 | 57.09 | 94.82 | 37 (298)
8.1 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 100 | GAIIx | 68258074 | 97.55 | 11.83 | 74.02 | 99.27 | 95.85 | 91.12 | 118.43 | 88.97 | 27 (339) | 7 (111)
8.2 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 100 | GAIIx | 73473916 | 98.14 | 12.33 | 76.76 | 99.29 | 96.16 | 91.86 | 132.35 | 88.36 | 27 (305)
9.1 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 75 | GAIIx | 75846314 | 93.93 | 13.18 | 77.52 | 98.91 | 94.66 | 89.18 | 107.43 | 87.95 | 20 (275) | 10 (129)
9.2 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 75 | GAIIx | 75309446 | 93.91 | 10.89 | 75.85 | 98.87 | 94.48 | 89.15 | 106.9 | 87.99 | 29 (295)
10.1 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 75 | GAIIx | 72550586 | 93.95 | 10.76 | 76.38 | 98.88 | 94.4 | 89.11 | 103.43 | 88.54 | 19 (262) | 3 (53)
10.2 | PE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 75 | GAIIx | 73431832 | 93.89 | 11.52 | 76.22 | 98.84 | 94.19 | 88.54 | 104.16 | 87.92 | 21 (267)
11.1 | inPE | SPRIworks (200-400 bp) | Ag Exome 50 Mb | PE | 100 | HiSeq | 115753164 | 98.66 | 24.24 | 72.25 | 98 | 87.09 | 78.17 | 96.34 | 78.17 | 69 (382) | 22 (155)
11.2 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 70952660 | 98.81 | 20.98 | 66.61 | 97.42 | 81.92 | 70 | 62.91 | 77.98 | 44 (300)
12.1 | inPE | SPRIworks (200-400 bp) | Ag Exome 50 Mb | PE | 100 | HiSeq | 109154198 | 98.46 | 16.25 | 72.26 | 98.03 | 87.24 | 78.44 | 100.07 | 77.64 | 60 (345) | 22 (58)
12.2 | inPE | SPRIworks (200-400 bp) | Ag Exome 50 Mb | PE | 100 | HiSeq | 102253336 | 98.42 | 20.02 | 71.89 | 97.91 | 85.95 | 76.31 | 89.59 | 78.07 | 57 (366)
13.1 | inPE | SPRIworks (200-400 bp) | NG EZ exome v1 | PE | 100 | HiSeq | 76173076 | 99.46 | 7.18 | 76.13 | 99.17 | 96.06 | 92.55 | 134.71 | 89.71 | 35 (310) | 13 (116)
13.2 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 75970274 | 98.33 | 11.47 | 58.75 | 97.36 | 81.53 | 69.87 | 66 | 76.4 | 43 (272)
14.1 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 70012852 | 97.1 | 20.22 | 69.93 | 97.62 | 83.87 | 72.72 | 64.83 | 80.28 | 41 (281) | 3 (21)
14.2 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 75415650 | 98.91 | 14.29 | 69.3 | 97.34 | 82.89 | 72.06 | 75.41 | 75.98 | 36 (261)
14.3 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 78039114 | 98.77 | 18.31 | 67.9 | 97.25 | 82.54 | 71.48 | 72.95 | 76.57 | 31 (307)
15.1 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 145810378 | 99.07 | 48.79 | 72.44 | 98.5 | 88.7 | 79.93 | 87.87 | 81.63 | 54 (328) | 7 (16)
15.2 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 71040142 | 98.2 | 17.99 | 70.61 | 97.71 | 84.28 | 73.37 | 69.57 | 79.65 | 42 (282)
15.3 | inPE | SPRIworks (200-400 bp) | Ag Exome v2 | PE | 100 | HiSeq | 77450768 | 97.78 | 15.7 | 72.21 | 97.72 | 84.8 | 74.47 | 79.91 | 78.36 | 44 (313)
Average |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 35 (284) | 9 (75)
aIndicates adaptor type (and protocol) used for library preparation. Paired-end (PE), single-end (SE), [NAME] (inPE)
bLibraries were prepared by hand (manual) or using the SPRIworks Fragment Library System (SPRIworks) incorporating size selection as indicated in parentheses
cExome enrichment was performed using either the NimbleGen Sequence Capture 2.1M Exome Array (NG exome array), EZ Exome Library version 1 or 2 (NG exome array v1 or v2) or Agilent SureSelect Human All Exon version 2 (Ag Exome v2) or 50 Mb (Ag Exome 50 Mb) libraries
dPercentage of reads that map and align to the reference genome and overlap with the targeted bases by at least one base.  The target regions differ according to the capture method used
eNumber of variants shared by all exome-sequenced family members (i.e. either 2 or 3)