Table 10 Complete Genomics LFR WGS Summary Metrics.
From: Extensive sequencing of seven human genomes to characterize benchmark reference materials
Subject | GM12878 (rep1) | GM12878 (rep2) | GM12878 (rep3) | AJ Son (GM24385) | AJ Mother (GM24143) | AJ Father (GM24149) |
|---|---|---|---|---|---|---|
Fully called genome fraction | 0.952 | 0.968 | 0.971 | 0.972 | 0.968 | 0.972 |
Gross mapping yield (Gb) | 363 | 362 | 368 | 365 | 371 | 363 |
Both mates mapped yield (Gb) | 317 | 311 | 316 | 310 | 325 | 312 |
Mate distribution mean | 310 | 290 | 290 | 275 | 277 | 282 |
SNP total count (PASS only) | 3308426 | 3410795 | 3428944 | 3443940 | 3461563 | 3418049 |
SNP transitions/transversions ratio (PASS only) | 2.134 | 2.134 | 2.134 | 2.135 | 2.134 | 2.140 |
N50 | 181 kb | 257 kb | 176 kb | 887 kb | 1661 kb | 734 kb |
Median Contig Length | 76 kb | 84 kb | 74 kb | 133 kb | 149 kb | 125 kb |
Fraction of Phased SNPs | 98.7% | 99.4% | 99.4% | 99.7% | 99.6% | 99.6% |
