Replicate
1 VF
Coverage Chromosome Position Reference Mutation Replicate
2 VF
Yes=2nd file within the range Replicate 3 VF Yes=3rd file within the range *Yes in Replicates 2 & 3
0.0105 956 18 48603079 C T         N/A
0.0131 915 18 48603083 G A         N/A
0.0118 847 7 55221909 G A         N/A
0.0543 847 7 55221915 T G 4.65% Y 5.34% Y Y
0.0201 845 7 55221903 C T         N/A
0.0195 822 7 55221878 C T         N/A
0.0122 817 20 36031726 C T         N/A
0.1077 808 20 36031767 C G 13.50% Y 11.38% Y Y
0.0137 805 20 36031725 C T         N/A
0.015 802 7 55221852 C T         N/A
0.055 782 7 55221914 C T 6.43% Y 6.81% Y Y
(Datawith coveragebetween782and227werehiddentocondensethetable)
0.0529 227 22 24176357 C G 4.39% Y #N/A #N/A #N/A
0.5286 227 4 55980239 C T         N/A
0.0724 221 13 28608234 C T 5.07% Y 8.19% Y Y
0.1244 217 11 108236191 A C 15.35% Y 13.92% Y Y
0.3704 216 11 108172365 T G         N/A
0.3519 216 7 128845112 C A         N/A
0.0605 215 19 17945623 G T 3.85% Y 5.24% Y Y
0.514 214 4 153249361 T C         N/A
0.1698 212 13 28608229 A T 12.98% Y 12.16% Y Y
0.0825 206 11 108173701 T G 9.39% Y 10.33% Y Y
0.099 202 13 28608233 T C 5.43% Y 6.86% Y Y
0.0714 196 2 29443612 C T #N/A #N/A 12.75% N #N/A
0.228 193 3 10188301 T G 23.05% Y 24.41% Y Y
0.0702 171 13 48941615 C A 11.73% Y 8.28% Y Y
0.0625 160 17 7579466 G C #N/A #N/A 12.93% N #N/A
0.0915 142 19 1220519 G A 9.40% Y 9.84% Y Y
0.1111 99 13 48941616 T C 20.00% N 13.13% Y N
*N/A=replicate1 VF>25%(0.25)
N=oneNandoneY,ortwoNsforthe tworeplicates
#N/A=oneormore#N/Awereidentifiedfromthe tworeplicates
Table 8: Calculation of percentage repeatability using empirically derived equation and a custom-designed The Concordance Calculator at low stringency (Ion Torrent Intra Run data).