i) Comparison of the numbers of mapped and unmapped reads to the H37Rv sequence or consensus sequence | ||||||||
---|---|---|---|---|---|---|---|---|
 | LineAge |  | H37Rv | Consensus sequence | Subtraction of ratio (%) | |||
Mapping stringency* | Local | End to end | Local | End to end | Local | End to end | ||
(CS minus H37Rv) | ||||||||
F092 | EAI | mapped | 681561 | 664376 | 684952 | 667250 | Â | Â |
 |  | unmapped | 22261 | 39446 | 18870 | 36572 |  |  |
 |  | ratio (%) | 96.837 | 94.395 | 97.319 | 94.804 | 0.482 | 0.408 |
J156 | EAI | mapped | 1680156 | 1650866 | 1689673 | 1658917 | Â | Â |
 |  | unmapped | 40162 | 69452 | 30645 | 61401 |  |  |
 |  | ratio (%) | 97.665 | 95.963 | 98.219 | 96.431 | 0.553 | 0.468 |
F038 | Haarlem, LAM, X etc. | mapped | 1024873 | 997301 | 1029625 | 1000714 | Â | Â |
 |  | unmapped | 75113 | 102685 | 70361 | 99272 |  |  |
 |  | ratio (%) | 93.171 | 90.665 | 93.603 | 90.975 | 0.432 | 0.310 |
F070 | Haarlem, LAM, X etc. | mapped | 858126 | 840921 | 861393 | 843463 | Â | Â |
 |  | unmapped | 27822 | 45027 | 24555 | 42485 |  |  |
 |  | ratio (%) | 96.860 | 94.918 | 97.228 | 95.205 | 0.369 | 0.287 |
J073 | Haarlem, LAM, X etc. | mapped | 1534315 | 1503494 | 1537891 | 1504256 | Â | Â |
 |  | unmapped | 11979 | 42800 | 8403 | 42038 |  |  |
 |  | ratio (%) | 99.225 | 97.232 | 99.457 | 97.281 | 0.231 | 0.049 |
J147 | Haarlem, LAM, X etc. | mapped | 847807 | 836269 | 849747 | 836489 | Â | Â |
 |  | unmapped | 11775 | 23313 | 9835 | 23093 |  |  |
 |  | ratio (%) | 98.630 | 97.288 | 98.856 | 97.313 | 0.226 | 0.026 |
F081 | other non-Beijing | mapped | 1004912 | 974425 | 1008107 | 976556 | Â | Â |
 |  | unmapped | 43978 | 74465 | 40783 | 72334 |  |  |
 |  | ratio (%) | 95.807 | 92.901 | 96.112 | 93.104 | 0.305 | 0.203 |
J020 | other non-Beijing | mapped | 1081365 | 1062537 | 1085065 | 1065704 | Â | Â |
 |  | unmapped | 11293 | 30121 | 7593 | 26954 |  |  |
 |  | ratio (%) | 98.966 | 97.243 | 99.305 | 97.533 | 0.339 | 0.290 |
J027 | other non-Beijing | mapped | 751633 | 741219 | 754861 | 744254 | Â | Â |
 |  | unmapped | 5259 | 15673 | 2031 | 12638 |  |  |
 |  | ratio (%) | 99.305 | 97.929 | 99.732 | 98.330 | 0.426 | 0.401 |
F022 | Ancestral Beijing | mapped | 1162270 | 1143243 | 1166545 | 1147960 | Â | Â |
 |  | unmapped | 26600 | 45627 | 22325 | 40910 |  |  |
 |  | ratio (%) | 97.763 | 96.162 | 98.122 | 96.559 | 0.360 | 0.397 |
J090 | Ancestral Beijing | mapped | 490815 | 484340 | 492424 | 486326 | Â | Â |
 |  | unmapped | 5153 | 11628 | 3544 | 9642 |  |  |
 |  | ratio (%) | 98.961 | 97.655 | 99.285 | 98.056 | 0.324 | 0.400 |
J002 | Ancestral Beijing | mapped | 736473 | 727044 | 739288 | 730539 | Â | Â |
 |  | unmapped | 5757 | 15186 | 2942 | 11691 |  |  |
 |  | ratio (%) | 99.224 | 97.954 | 99.604 | 98.425 | 0.379 | 0.471 |
J029 | Modern Beijing | mapped | 953792 | 936476 | 957539 | 941221 | Â | Â |
 |  | unmapped | 10220 | 27536 | 6473 | 22791 |  |  |
 |  | ratio (%) | 98.940 | 97.144 | 99.329 | 97.636 | 0.389 | 0.492 |
F076 | Modern Beijing | mapped | 532526 | 519473 | 534742 | 522431 | Â | Â |
 |  | unmapped | 16374 | 29427 | 14158 | 26469 |  |  |
 |  | ratio (%) | 97.017 | 94.639 | 97.421 | 95.178 | 0.404 | 0.539 |
J111 | Modern Beijing | mapped | 719693 | 708076 | 722895 | 712304 | Â | Â |
 |  | unmapped | 14341 | 25958 | 11139 | 21730 |  |  |
 |  | ratio (%) | 98.046 | 96.464 | 98.482 | 97.040 | 0.436 | 0.576 |
 | ii) Comparison of mappping frequency ratio (%) among the MTBC lineanges |  |  |  |  | |||
 |  | EAI | Haarlem, LAM, X etc. | other non-Beijing |  |  |  |  |
 | Haarlem, LAM, X etc. | ns | - | - |  |  |  |  |
 | other non-Beijing | ns | ns | - |  |  |  |  |
 | Beijing | P < 0.05 | ns | ns |  |  |  |  |