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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