Table 2 Mean of alignment results from 15 samples from the 1000 Genomes data when aligning to (1) the reference genome sequence of chromosome 6 (column GRC37) and (2) the population graph created from the 5008 haplotypes, for both CHOP/BWA and vg with and without haplotyping
From: CHOP: haplotype-aware path indexing in population graphs
| Â | 1000 Genomes samples, read length = 100 | Â | Â | Â | |||
|---|---|---|---|---|---|---|---|
Alignment criteria | BWA | CHOP/BWA | vg | vg | vg + BGWT | GraphAligner | GraphAligner |
| Â | GRC37 | Graph (n = 2504) | GRC37 | Graph (n = 2504) | Graph (n = 2504) | GRC37 | Graph (n = 2504) |
Reads aligned | 2,542,399 | 2,543,522 (+ 0.044%) | 2,684,925 | 2,726,051 (+ 1.532%) | 2,717,972 (+ 1.231%) | 2,664,609 | 2,630,670 (− 1.274%) |
Reads unaligned | 483,670 | 482,548 (− 0.232%) | 341,144 | 300,018 (− 12.056%) | 308,098 (− 9.687%) | 361,460 | 395,399 (+ 9.389%) |
Reads perfectly aligned | 1,794,564 | 1,977,952 (+ 10.219%) | 1,807,158 | 1,993,967 (+ 10.337%) | 1,993,469 (+ 10.310%) | 1,789,327 | 1,950,435 (+ 9.004%) |
Bases aligned | 251,122,992 | 251,516,725 (+ 0.157%) | 254,518,323 | 255,911,471 (+ 0.547%) | 255,578,370 (+ 0.416%) | 258,684,466 | 256,773,126 (− 0.739%) |
Bases unaligned | 51,439,949 | 51,070,534 (− 0.718%) | 48,029,518 | 46,654,663 (− 2.863%) | 46,995,159 (− 2.154%) | 41,030,266 | 43,649,514 (+ 6.383%) |
Bases unaligned from clipped reads | 1,801,947 | 1,846,687 (+ 2.483%) | 12,716,162 | 15,699,089 (+ 23.458%) | 15,245,035 (+ 19.887%) | 203,221 | 177,659 (− 12.578%) |
Bases mismatched | 1,270,981 | 969,087 (− 23.753%) | 1,198,917 | 953,800 (− 20.445%) | 940,371 (− 21.565%) | 4,681,045 | 3,931,955 (− 16.003%) |
Bases inserted | 43,979 | 19,661 (− 55.296%) | 59,078 | 40,786 (−30.962%) | 33,391 (− 43.480%) | 2,541,719 | 1,925,093 (− 24.260%) |
Bases deleted | 61,659 | 32,355 (− 47.526%) | 73,131 | 44,555 (− 39.075%) | 41,040 (− 43.882%) | 464,085 | 415,508 (− 10.467%) |
Time alignment (s) | 544 | 1807 | 19,996 | 10,436 | 10,871 | 916 | 2102 |
Memory alignment (MB) | 412 | 5534 | 837 | 3296 | 4389 | 3047 | 14,446 |
Time indexing (s) | 186 | CHOP, 43,625; BWA, 3256 | 37 | 5751 | 33,619 | NA | NA |
Memory indexing (MB) | 245 | CHOP, 56,969; BWA, 3813 | 269 | 45,670 | 45,868 | NA | NA |