Table 1.

Summary of mate-paired tag libraries.

SamplesSingle tag analysesMate-paired tag analyses
Number of
beads*
Number
of tags
matching human
genome
Total
bases
sequenced
(bp)
Expected
coverage
per
3-kb bin
Number of
mate-paired
tags matching
human genome
Distance
between
mate-paired
tags (bp)
Total
physical
coverage by
mate-paired
tags (bp)
Expected
genome
coverage
Colon cancer
Co108
tumor
526,209,780121,527,7073,038,192,67512221,899,809137130,024,693,71410.0
Co108
normal
328,599,03386,032,2532,150,806,3258611,694,361125414,665,530,8044.9
Co84
tumor
677,137,128256,065,4376,401,635,92525658,678,410148887,292,060,00629.1
Co84
normal
486,663,520218,280,1465,457,003,65021859,019,031138481,690,396,37927.2
Hx402
tumor
523,745,015198,342,7494,958,568,72519843,457,431162970,789,547,65323.6
Hx403
tumor
475,658,760164,061,9384,101,548,45016437,123,395170563,295,388,47521.1
Breast cancer
B7
tumor
840,979,999281,027,2747,025,681,85028127,548,989122033,604,662,40411.2
B7
normal
705,704,265253,482,2626,337,056,55025357,878,644140481,271,654,77027.1
B5
tumor
444,249,217147,612,9413,690,323,52514829,961,045119335,730,144,65111.9
B5
normal
549,237,156220,669,7955,516,744,87522153,611,974120564,591,276,02521.5

*Number of beads corresponds to the number of magnetic beads containing clonally amplified DNA fragments and represents the maximal number of raw sequence reads for each run.