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Table 1 Sequencing and coverage statistics for all paired-read libraries

From: Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing

Library name* Sequenced pairs Non-duplicate pairs (%) Unique, consistently mapped pairs (%) Median insert size (bp) Physical coverage (x-fold) 5 M reads coverage (x-fold) PCR cycles ** Relative complexity *** inconsistent pairs forming clusters inconsistent inter-chromosomal pairs forming clusters
PE 160 M 151 M (95%) 131 M (87%) 166 8.5 0.34 5 >131 M 9.5% 2.0%
3 kb 17.7 M 16.3 M (92%) 15.2 M (93%) 3,208 50 6 14 4.6 M 24.0% 3.2%
5 kb_a 11.9 M 6.0 M (51%) 5.5 M (92%) 5,696 11 10.1 18 4.7 M 46.5% 3.7%
5 kb_b 16.7 M 14.7 M (88%) 14.0 M (95%) 5,811 28 10.1 13 >16.7 M 47.5% 4.6%
8 kb_a 20.8 M 8.6 M (41%) 7.8 M (91%) 8,293 25 16.2 14 5.7 M 58.4% 6.9%
8 kb_b 11.8 M 11.2 M (95%) 10.6 M (95%) 8,160 34 16.2 13 >11.8 M 50.6% 5.5%
15 kb_a 31.7 M 1.7 M (5%) 1.0 M (60%) 14,561 6 30.3 21 0.6 M 60.8% 7.6%
15 kb_b 11.6 M 1.6 M (14%) 1.2 M (73%) 13,556 7 30.3 21 0.7 M 23.2% 3.2%
20 kb 13.3 M 6.7 M (51%) 5.9 M (87%) 19,375 48 40.5 14 4.9 M 41.8% 4.7%
25 kb 56.9 M 2.3 M (4%) 1.1 M (49%) 25,871 11 50.6 17 0.7 M 51.9% 5.4%
TOTAL 352.4 M 220.1 M (62%) 193.3 M (88%)   228.5      
  1. * The _b samples are retrieved from a replicate experiment using an independent DNA isolate from the same animal.
  2. ** Number of PCR cycles required to retrieve sufficient library molecules in the final adapter-mediated PCR.
  3. *** Complexity is defined as minimal sequencing depth (in million clones) at which over half of the pairs are clonal.