Table 1.
Examples of integer copy number inference from PRT and ratio data
| Sample ID | MLCN | Minimum ratio (MR) | MLT1A0 PRT | DEFA4 PRT | indel5 ratio | indel5 integers | DefHae3 ratio | DefHae3 integers | 7bpdup ratio | 7bpdup integers |
|---|---|---|---|---|---|---|---|---|---|---|
| NA12751 | 7 | 511.47 | 7.07 | 7.03 | 1.32 | 4:3 | 2.38 | 5:2 | 0.41 | 2:5 |
| C0052 | 8 | 152.11 | 8.30 | 7.70 | 1.07 | 4:4 | 5.66 | 7:1 | 0.60 | 3:5 |
| NA12749 | 5 | 21.99 | 5.71 | 5.21 | (No data) | - | 3.70 | 4:1 | 3.74 | 4:1 |
| C0157 | 9 | 10.50 | 9.09 | 9.02 | 1.18 | 5:4 | 6.12 | 8:1 | 0.78 | 4:5 |
| NA12778 | 6 | 3.26 | (No data) | 7.59 | 1.12 | 3:3 | 5.49 | 5:1 | 0.21 | 1:5 |
Examples of copy number inference from PRT and ratio data. For each sample the table shows the MLCN (maximum likelihood copy number) derived by combining information from different measures (see text and Table 2) and the minimum ratio (MR) score indicating the confidence with which that copy number is assigned. For the three ratio tests (indel5, DefHae3 and 7bpdup), the measured ratio is shown alongside the integer interpretation derived from the MLCN that best fits the observed ratio. Samples are arranged in decreasing order of confidence, as reflected in decreasing values of the minimum ratio (MR).