Skip to main content

Table 3 Comparison of SH3TC2 alleles in six exome sequencing experiments and one whole-genome sequencing.

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

Instrument   p.M1? Ratio p.Y169H Ratio p.R954x Ratio
GAII (Ex1) RR 47 0.48 90 0.50 63 0.47
  VR 66 0.58 90 0.50 71 0.53
  TR 113 - 180 - 134 -
GAII (Ex2) RR 50 0.48 79 0.45 45 0.39
  VR 54 0.52 95 0.55 69 0.61
  TR 104 - 174 - 114 -
HiSeq (Ex1) RR 71 0.42 100 0.48 54 0.47
  VR 98 0.58 109 0.52 61 0.53
  TR 169 - 209 - 115 -
HiSeq (Ex2) RR 70 0.42 90 0.44 72 0.49
  VR 97 0.58 114 0.56 76 0.51
  TR 167 - 204 - 148 -
PGM (Ex) RR 19 0.37 55 0.55 45 0.58
  VR 33 0.63 45 0.45 33 0.42
  TR 52 - 100 - 78 -
Proton (Ex) RR 58 0.55 79 0.50 35 0.56
  VR 48 0.45 80 0.50 28 0.44
  TR 108 - 159 - 63 -
HiSeq-WGS RR 29 0.60 25 0.43 32 0.48
  VR 19 0.40 33 0.57 34 0.52
  TR 48 - 58 - 66 -
  1. RR: number of reads calling the reference base; TR: total number of reads at that position; VR: number of reads calling the variant base. The ratio columns reflect the fraction of reads that called either the reference base or the read base over the total number of reads for that position.