Table 1:
Number of queries out of 100,000,000 in each benchmark set for which a mapping at the target number of errors is not reported
| Method | 0.5% | 1% | 1.5% | 2% | 2.5% | 3% | 4% |
|---|---|---|---|---|---|---|---|
| 100-bp paired sets | |||||||
| GEM fast | 208,716 | 452,079 | 687,939 | 915,017 | 1,152,014 | 1,420,600 | 2,144,373 |
| GEM sensitive | 24,808 | 54,032 | 92,371 | 142,406 | 204,455 | 281,705 | 523,960 |
| BWA-MEM default | 225,610 | 614,532 | 1,230,792 | 2,097,907 | 3,239,775 | 4,681,048 | 8,563,643 |
| BWA-MEM custom | 2,359,073 | 2,384,496 | 2,419,891 | 2,466,556 | 2,527,910 | 2,607,907 | 2,835,866 |
| SRPRISM fast | 616,704 | 830,673 | 1,785,953 | 4,346,647 | 9,318,663 | 16,987,001 | 38,310,302 |
| SRPRISM sensitive | 13,781 | 161,295 | 978,406 | 3,371,025 | 8,198,853 | 15,783,121 | 37,192,459 |
| (check count) | (2) | (2) | (13) | (17) | (18) | (27) | (32) |
| Hobbes | 13,791 | 161,310 | 978,421 | 3,371,041 | 8,198,870 | 15,783,133 | 37,192,468 |
| Yara | 2,028,722 | 2,320,285 | 3,218,186 | 5,616,159 | 10,368,429 | 17,790,749 | 38,676,640 |
| Kart | 3,099,642 | 4,906,886 | 7,970,113 | 12,270,554 | 17,617,775 | 23,734,421 | 37,223,055 |
| STAR | 3,936,831 | 5,998,191 | 8,153,960 | 10,520,656 | 13,461,104 | 17,566,471 | 30,942,844 |
| Bowtie2 | 566,714 | 824,542 | 1,216,097 | 1,659,296 | 2,180,881 | 2,783,325 | 4,344,807 |
| 250-bp paired sets | |||||||
| GEM fast | 191,675 | 309,943 | 396,546 | 493,401 | 620,435 | 783,967 | 1,250,672 |
| GEM sensitive | 17,437 | 38,105 | 73,760 | 128,479 | 205,774 | 309,672 | 620,641 |
| BWA-MEM default | 175,984 | 512,561 | 1,071,537 | 1,864,593 | 2,917,694 | 4,234,163 | 7,718,972 |
| BWA-MEM custom | 4,163,355 | 4,166,258 | 4,180,166 | 4,198,419 | 4,216,046 | 4,241,512 | 4,301,237 |
| SRPRISM fast | 7,243 | 10,171 | 20,220 | 82,247 | 485,610 | 2,158,312 | 15,963,870 |
| SRPRISM sensitive | 6 | 103 | 2,896 | 52,640 | 435,848 | 2,082,873 | 15,842,838 |
| (check count) | (0) | (1) | (0) | (2) | (4) | (7) | (6) |
| Hobbes | 712,059 | 9,957,606 | 34,283,316 | 62,109,460 | 81,094,426 | 90,103,730 | 94,380,319 |
| Yara | 1,118,568 | 1,139,838 | 1,182,725 | 1,584,865 | 3,609,820 | 9,519,961 | 37,597,089 |
| Kart | 3,291,334 | 6,529,283 | 12,026,850 | 19,338,546 | 27,932,293 | 37,124,040 | 55,155,698 |
| STAR | 3,705,691 | 7,288,696 | 20,709,476 | 46,098,586 | 70,500,124 | 85,216,290 | 93,852,773 |
| Bowtie2 | 511,367 | 1,029,144 | 1,575,666 | 1,944,531 | 2,258,863 | 2,568,040 | 3,311,748 |
| 100-bp single sets | |||||||
| GEM fast | 697,818 | 1,238,906 | 1,799,896 | 2,431,653 | 3,193,987 | 4,126,182 | 6,625,844 |
| GEM sensitive | 18,479 | 41,393 | 68,604 | 99,672 | 137,949 | 190,986 | 364,521 |
| BWA-MEM default | 131,829 | 353,621 | 708,158 | 1,211,188 | 1,883,318 | 2,750,676 | 5,143,324 |
| BWA-MEM custom | 41,331 | 89,456 | 161,560 | 259,535 | 388,985 | 554,852 | 1,017,491 |
| SRPRISM fast | 354,827 | 482,556 | 970,542 | 2,261,776 | 4,824,603 | 8,930,551 | 21,561,640 |
| SRPRISM sensitive | 6,871 | 79,825 | 487,266 | 1,686,967 | 4,163,766 | 8,201,636 | 20,791,635 |
| (check count) | (5) | (3) | (6) | (9) | (13) | (14) | (13) |
| Hobbes | 6,879 | 79,836 | 487,278 | 1,686,978 | 4,163,781 | 8,201,647 | 20,791,648 |
| Yara | 7,045 | 80,320 | 488,388 | 1,688,898 | 4,166,532 | 8,205,171 | 20,796,339 |
| Kart | 2,316,648 | 3,458,734 | 5,354,805 | 8,018,703 | 11,393,479 | 15,370,874 | 24,641,561 |
| STAR | 2,933,574 | 3,858,421 | 4,892,676 | 6,021,576 | 7,255,494 | 8,607,920 | 11,708,200 |
| Bowtie2 | 434,413 | 1,162,865 | 2,147,595 | 3,088,132 | 4,031,885 | 5,019,518 | 7,278,163 |
| 250-bp single sets | |||||||
| GEM fast | 470,499 | 613,415 | 711,556 | 829,955 | 984,829 | 1,185,478 | 1,753,151 |
| GEM sensitive | 12,230 | 21,540 | 35,493 | 58,151 | 92,135 | 141,456 | 294,110 |
| BWA-MEM default | 96,944 | 274,979 | 563,872 | 973,153 | 1,515,439 | 2,195,157 | 4,019,429 |
| BWA-MEM custom | 89,619 | 98,956 | 113,424 | 131,055 | 153,179 | 180,745 | 252,940 |
| SRPRISM fast | 6,119 | 8,583 | 14,575 | 46,442 | 249,263 | 1,092,460 | 8,346,408 |
| SRPRISM sensitive | 2 | 50 | 1,505 | 26,337 | 217,830 | 1,046,440 | 8,270,701 |
| (check count) | (0) | (0) | (1) | (2) | (2) | (1) | (2) |
| Hobbes | 355,895 | 5,112,610 | 19,046,975 | 39,121,004 | 58,784,299 | 73,835,948 | 89,223,792 |
| Yara | 17 | 671 | 20,079 | 229,846 | 1,278,929 | 4,380,059 | 20,794,991 |
| Kart | 1,974,474 | 3,801,390 | 6,906,889 | 11,136,617 | 16,332,521 | 22,220,722 | 35,305,069 |
| STAR | 2,093,088 | 3,075,609 | 4,234,139 | 6,327,695 | 10,836,887 | 19,020,755 | 44,485,933 |
| Bowtie2 | 628,816 | 1,231,834 | 1,747,783 | 2,077,950 | 2,361,942 | 2,636,580 | 3,246,201 |
For each benchmark set, cell in bold italic has the best result (lowest number) and cell in bold has the second best result among all methods tested. For SRPRISM sensitive mode, numbers in rows labeled “(check count)” give the number of queries where a mapping at the target number of errors is expected to be found but was not. All such cases were found to be due to an error in the software that reported the target number of errors. Every read for which SRPRISM sensitive mode found the target number of errors but SRPRISM fast mode did not had the XA:i flag set to 0 in the alignment of SRPRISM fast mode to indicate that an exhaustive search was not done on that read in the fast mode.