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. |
|||||||||
|
Raphael et al. Genome Biology 2008 9:R59 doi:10.1186/gb-2008-9-3-r59 |
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