Table 1 Mean of alignment results across all 10 hold-out sample alignments to (1) the reference genome H37Rv (H37Rv columns) and (2) the 400 MTB genomes graph (graph columns) for both CHOP/BWA and vg with and without haplotyping to align the reads (note that when aligning only to H37Rv, CHOP is not used)
From: CHOP: haplotype-aware path indexing in population graphs
| Â | All TB hold-out samples, read length = 101 | Â | Â | Â | |||
|---|---|---|---|---|---|---|---|
Alignment criteria | BWA | CHOP/BWA | vg | vg | vg + GBWT | HiSat2 | HiSat2 |
| Â | H37RV | Graph (n = 400) | H37RV | Graph (n = 400) | Graph (n = 400) | H37RV | Graph (n = 400) |
Reads aligned | 6,160,920 | 6,162,033 (+ 0.018%) | 6,241,270 | 6,245,907 (+ 0.074%) | 6,244,004 (+ 0.044%) | 5,536,194 | 5,489,149 (− 0.850%) |
Reads unaligned | 360,236 | 359,123 (− 0.309%) | 279,886 | 275,249 (− 1.657%) | 277,152 (− 0.977%) | 984,962 | 1,032,007 (+ 4.776%) |
Reads perfectly aligned | 4,048,774 | 4,142,052 (+ 2.304%) | 4,048,774 | 4,153,217 (+ 2.580%) | 4,153,124 (+ 2.577%) | 4,056,850 | 4,113,818 (+ 1.404%) |
Bases aligned | 596,380,132 | 596,611,260 (+ 0.039%) | 599,244,753 | 599,601,399 (+ 0.060%) | 599,528,267 (+ 0.047%) | 553,338,901 | 548,757,802 (− 0.828%) |
Bases unaligned | 62,191,423 | 61,960,355 (− 0.372%) | 59,307,655 | 58,949,429 (− 0.604%) | 59,023,102 (− 0.480%) | 105,271,191 | 109,852,201 (+ 4.352%) |
Bases unaligned from clipped reads | 22,349,569 | 22,380,472 (+ 0.138%) | 27,442,533 | 27,690,552 (+ 0.904%) | 27,575,464 (+ 0.484%) | 3,625,336 | 3,589,573 (− 0.986%) |
Bases mismatched | 3,458,029 | 3,308,480 (− 4.325%) | 3,596,667 | 3,458,707 (− 3.836%) | 3,455,296 (− 3.931%) | 2,164,703 | 2,029,911 (− 6.227%) |
Bases inserted | 65,210 | 65,151 (− 0.090%) | 84,358 | 85,938 (+ 1.874%) | 85,397 (+ 1.232%) | 26,674 | 26,763 (+ 0.334%) |
Bases deleted | 52,272 | 51,165 (− 2.118%) | 70,324 | 72,082 (+ 2.500%) | 70,347 (+ 0.033%) | 11,793 | 11,756 (− 0.317%) |
Non-primary alignments | 246,092 | 246,540 (+ 0.182%) | 539,309 | 724,904 (+ 34.414%) | 724,613 (+ 34.360%) | 969,452 | 755,436 (− 22.076%) |
Time (s) | 533 | 721 | 10,711 | 4457 | 4540 | 312 | 517 |