Table 6.
Lengths of segments without switches obtained with WGS SNPs selected with more traditional filtering rules for the two phasing strategiesa, whether correctly or wrongly phased or both (all)
| WGS-P1 | WGS-P2 | |||||||
|---|---|---|---|---|---|---|---|---|
| All | Correct | Wrong | All | Correct | Wrong | |||
| Original segments | ||||||||
| Physical lengthb | ||||||||
| Avg | 0.50 | 0.49 | 0.50 | 0.51 | 0.99 | 0.04 | ||
| Med | 346 bp | 297 bp | 404 bp | 396 bp | 223.51 kb | 1 bp | ||
| Max | 34.88 | 34.88 | 21.33 | 25.64 | 25.64 | 14.65 | ||
| Proportion of singletonsc | 40.76% | 41.05% | 40.48% | 40.61% | 16.11% | 65.31% | ||
| Number of phasable SNPs per segment | ||||||||
| Avg | 373.70 | 370.72 | 376.69 | 384.98 | 758.49 | 8.40 | ||
| Med | 2 | 2 | 2 | 2 | 131 | 1 | ||
| Max | 29,712 | 29,712 | 26,646 | 32,839 | 32,839 | 1813 | ||
| Number of SNPs per segment | ||||||||
| Avg | 2618.11 | 2593.29 | 2642.94 | 2704.68 | 5179.74 | 209.22 | ||
| Med | 4 | 4 | 4 | 4 | 1228.5 | 1 | ||
| Max | 158,630 | 158,630 | 113,469 | 134,130 | 134,130 | 84,929 | ||
| After discarding singletonsc | ||||||||
| Physical lengthb | ||||||||
| Avg | 1.88 | 1.87 | 1.9 | 1.94 | 3.64 | 0.19 | ||
| Med | 0.05 | 0.05 | 0.05 | 0.03 | 1.04 | 1.92 kb | ||
| Max | 63.16 | 55.98 | 63.16 | 85.72 | 85.72 | 31.87 | ||
| Number of phasable SNPs per segment | ||||||||
| Avg | 1335.70 | 1325.27 | 1346.13 | 1373.47 | 2675.79 | 28.52 | ||
| Med | 14 | 14 | 14 | 10 | 659 | 3 | ||
| Max | 74,067 | 57,000 | 74,067 | 97,334 | 97,334 | 2787 | ||
| Number of SNPs per segment | ||||||||
| Avg | 9895.56 | 9823.59 | 9967.51 | 10,208.87 | 19,121.57 | 1004.46 | ||
| Med | 255 | 241 | 266 | 153 | 5657 | 13 | ||
| Max | 325,812 | 293,893 | 325,812 | 437,121 | 437,121 | 141,991 | ||
| After discarding segments with less than five phasable SNPs and shorter than 5 kb | ||||||||
| Physical lengthb | ||||||||
| Avg | 4.34 | 4.31 | 4.36 | 4.84 | 8.84 | 0.50 | ||
| Med | 0.95 | 0.95 | 0.95 | 0.44 | 3.52 | 494.45 kb | ||
| Max | 121.41 | 121.41 | 116.11 | 121.41 | 121.41 | 33.07 | ||
| Number of phasable SNPs per segment | ||||||||
| Avg | 3045.22 | 3024.33 | 3066.06 | 3388.28 | 6444.96 | 69.46 | ||
| Med | 318 | 310.5 | 325 | 78 | 2311 | 10 | ||
| Max | 110,344 | 110,344 | 86,208 | 112,056 | 112,056 | 2793 | ||
| Number of SNPs per segment | ||||||||
| Avg | 22,773.56 | 22,633.66 | 22,913.14 | 25,438.65 | 46,480.17 | 2592.66 | ||
| Med | 4951 | 4939 | 4971 | 2206 | 19,046 | 254 | ||
| Max | 605,700 | 605,700 | 601,045 | 653,272 | 653,272 | 160,715 | ||
A segment is defined as a run of consecutive phasable SNPs without switches
aWGS-P1: phased with LD information only; WGS-P2: phased with both LD and familial information
bUnless specified, all length units are in Mb
c“Singleton” refers to segments that contain only one SNP