Table 2.
Results of end sequencing and mapping of each library
| MCF7 | BT474 | SKBR3 | Breast | Breast.2 | Ovary | Prostate | Brain | Normal | |
|---|---|---|---|---|---|---|---|---|---|
| Library name | MCF7_1 | CHORI-518 | CHORI-520 | B421 | CHORI514 | CHORI510 | PM1 | IGBR | K0241 |
| Mapped clones (n) | 12,143 | 8,044 | 7,363 | 6,972 | 5,678 | 3,946 | 3,499 | 3,238 | 609 |
| Unique mapped clones (n) | 11,492 | 7,547 | 6,950 | 6,540 | 5,381 | 3,714 | 3,296 | 3,051 | 568 |
| Valid pairs (n) | 11,001 | 7,361 | 6,763 | 6,376 | 5,268 | 3,627 | 3,200 | 2,984 | 560 |
| Contigs (n) | 6,323 | 4,135 | 4,171 | 4,365 | 3,450 | 2,877 | 2,747 | 2,573 | 548 |
| Contig coverage | 0.324 | 0.327 | 0.274 | 0.233 | 0.243 | 0.155 | 0.104 | 0.103 | 0.019 |
| Invalid pairs (n) | 491 | 186 | 187 | 164 | 113 | 87 | 96 | 67 | 8 |
| Fraction invalid | 0.043 | 0.025 | 0.027 | 0.025 | 0.021 | 0.023 | 0.029 | 0.022 | 0.014 |
| P value | 4.10 × e-04 | 0.056 | 0.032 | 0.051 | 0.133 | 0.080 | 0.020 | 0.113 | NA |
| Number clusters (n) | 36 | 26 | 24 | 2 | 7 | 2 | 2 | 0 | 0 |
| Invalid pairs in clusters (n) | 164 | 61 | 64 | 4 | 24 | 4 | 4 | 0 | 0 |
The fraction of invalid pairs is calculated relative to the number of uniquely mapped pairs. The P value is the probability that the fraction of invalid pairs is the same as observed in the normal library, using a sample proportion test with pooled variance.