Table 1

Properties of datasets from different sequencing centers
SC BCM BI WU
Total sample count 117 352 161 93
Sample count after quality control 106 349 110 82
Technology Illumina 454 Illumina Illumina
Duplicate rate 0.21 0.30 0.50 0.72
Mapping quality (mean) 50 33 45 51
Base coverage(mean ± standard deviation) 56 ± 34 23 ± 12 70 ± 61 29 ± 9
Read depth per gene(mean ± standard deviation) 2309 ± 3166 106 ± 171 1329 ± 2053 977 ± 1382
MRD(mean ± standard deviation) 1710 ± 1073 97 ± 52 1070 ± 803 599 ± 164
Number of exons 8174 8174 8174 8174
Exons overlapped with segmental duplication regions 458 (5.6%) 458 (5.6%) 458 (5.6%) 458 (5.6%)
Number of genes (passing QC) 862 439 739 1
Genes overlapped with segmental duplication regions 29 (3.3%) 11(2.5%) 23(3.1%) 0(0.0%)
Over-dispersion factor(mean ± standard deviation) 7.9 ± 8.2 2.1 ± 1.1 6.4 ± 5.5 N/A
Quality index(mean ± standard deviation) 9.4 ± 8.8 5.5 ± 2.3 7.6 ± 5.6 N/A
Expected detection sensitivity based on quality index 0.46 0.20 0.41 N/A
Number of callsh = 0.65 either with or without a neighboring call 36 4 56 N/A
Number of callsh = 0.1 either with a neighboring call 17 0 11 N/A

Wu et al.

Wu et al. BMC Bioinformatics 2012 13:305   doi:10.1186/1471-2105-13-305

Open Data