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Table 1 SNV identified by replicated ES of CMT proband.

From: Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy

Platform GAII-1 GAII-2 HiSeq-1 HiSeq-2 PGM Proton WGS-SOLID WGS-HiSeq
Total reads produced 117,685,348 107,207,362 119,508,046 118,716,380 41,268,598 71,113,537 2,469,936,140 1,479,177,846
Duplicate reads (%) 4.98 3.63 5.86 5.74 25.10 19.34 5.00 2.29
Total reads aligned (%) 97.80 98.66 96.76 97.09 99.16 98.83 58.12 96.57
Aligned reads on target (%) 64.90 69.70 70.59 70.66 60.81 71.66 N/A N/A
Average coverage 138x 137x 170x 169x 65x 93x 29.6x 47.6x
Median coverage 110x 111x 140x 139x 60x 80x N/A 40x
Targets hit (%) 99.42 99.32 99.42 99.40 99.22 99.29 N/A N/A
Bases targeted 35,432,211 35,432,211 35,432,211 35,432,211 35,432,211 35,432,211 N/A N/A
Targeted bases with 10+ coverage (%) 97.58 97.49 97.98 97.99 95.84 94.64 N/A N/A
Targeted bases with 20+ coverage (%) 96.19 96.18 97.23 97.21 92.28 91.28 N/A N/A
Targeted bases with 40+ coverage (%) 90.60 91.08 94.59 94.53 75.19 80.75 N/A N/A
Total SNPs 102,444 91,661 92,553 91,484 41,958 57,243 3,420,306 4,016,486
cSNPs (n) 23,321 22,869 23,017 22,980 20,372 22,079 18,829 24,475
nsSNPs (n) 11,491 11,217 11,288 11,252 11,363 10,821 9,069 12,370
Total c_inDels 8,879 8,249 9,576 9,375 N/A N/A N/A 10,439