Table 4.
Lengths of segments without switches of the trusted set of WGS SNPs 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 | 3.01 | 2.96 | 3.07 | 3.19 | 6.11 | 84.99 kb |
| Med | 4.58 kb | 4.75 kb | 4.33 kb | 3.38 kb | 1.74 | 1 bp |
| Max | 150.73 | 150.73 | 123.75 | 116.39 | 116.39 | 42.76 |
| Proportion of singletonsc | 37.52% | 37.53% | 37.51% | 38.82% | 12.18% | 67.24% |
| Number of phasable SNPs per segment | ||||||
| Avg | 1048.45 | 1041.75 | 1055.17 | 1098.05 | 2119.04 | 8.39 |
| Med | 4 | 4 | 4 | 3 | 644 | 1 |
| Max | 55,553 | 55,553 | 50,217 | 51,340 | 51,340 | 835 |
| Number of SNPs per segment | ||||||
| Avg | 6232.95 | 6134.89 | 6331.09 | 6612.58 | 12,639.78 | 179.99 |
| Med | 12 | 13 | 12 | 8.5 | 3641 | 1 |
| Max | 308,884 | 308,884 | 240,332 | 231,051 | 231,051 | 85,165 |
| After discarding singletonsc | ||||||
| Physical lengthb | ||||||
| Avg | 9.48 | 9.28 | 9.67 | 11.02 | 19.46 | 0.36 |
| Med | 1.25 | 1.39 | 1.12 | 0.26 | 6.39 | 0.01 |
| Max | 154.47 | 154.47 | 147.3 | 147.3 | 147.3 | 42.76 |
| Number of phasable SNPs per segment | ||||||
| Avg | 3185.72 | 3163.65 | 3207.84 | 3652.87 | 6524.06 | 28.54 |
| Med | 367 | 418 | 314 | 59 | 2352 | 4 |
| Max | 67,776 | 67,776 | 60,281 | 67,776 | 67,776 | 1452 |
| Number of SNPs per segment | ||||||
| Avg | 19,586.14 | 19,210.75 | 19,962.22 | 22,778.53 | 40,230.9 | 748.21 |
| Med | 2555 | 2925.5 | 2306 | 523 | 13,713 | 15 |
| Max | 318,618 | 318,618 | 304,742 | 304,742 | 304,742 | 85,165 |
| After discarding segments with less than five phasable SNPs and shorter than 5 kb | ||||||
| Physical lengthb | ||||||
| Avg | 14.78 | 14.46 | 15.11 | 19.36 | 31.64 | 0.72 |
| Med | 4.62 | 4.72 | 4.51 | 2.28 | 19.59 | 0.06 |
| Max | 158.12 | 158.1 | 158.12 | 158.24 | 158.24 | 42.76 |
| Number of phasable SNPs per segment | ||||||
| Avg | 4956.66 | 4911.73 | 5001.86 | 6400.99 | 10,581.41 | 53.68 |
| Med | 1489 | 1584 | 1401 | 522 | 6580 | 13 |
| Max | 73,348 | 73,348 | 60,625 | 67,776 | 67,776 | 1452 |
| Number of SNPs per segment | ||||||
| Avg | 30,549.61 | 29,916.85 | 31,186.28 | 40,033.57 | 65,412.51 | 1499.57 |
| Med | 9884 | 10,364 | 9497.5 | 4913 | 41,646 | 138 |
| Max | 327,738 | 327,706 | 327,738 | 327,914 | 327,914 | 85,165 |
A segment is defined as a run of consecutive phasable SNPs without switches
a WGS-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