File S5 Sample ID Population 2A 2B 2C 3A 3B 3C 4A

File S5 Sample ID 533 1389 738 186 957 311 1383 483 534 10 745 1460 994 1519 1268 492 536 11 750 1735 1021 330 1274 1575 538 1592 756 197 1032 333 1256 1784 540 20 765 198 1035 1529 1257 486 542 1595 784 206 1026 1766 1260 1785 545 26 785 1736 1061 351 1275 494 547 30 706 1730 1063 1681 1295 1577 549 1597 710 1669 1070 1682 1297 508 551 33 720 1732 1077 361 1300 510 554 42 721 170 1080 363 1313 517 556 43

Population Clinical Env Clinical Air Clinical Air Clinical Air Clinical Air Clinical Env Clinical Env Clinical Air Clinical Air Clinical Water Clinical Air Clinical Env Clinical Soil Clinical Air Clinical Air Clinical Water Clinical Air Clinical Air Clinical Env Clinical Air Clinical Soil Clinical Air Clinical Water Clinical Water Clinical Air Clinical Water Clinical Air Clinical Air Clinical Air Clinical Water Clinical Soil Clinical Env Clinical Soil Clinical Soil Clinical Soil Clinical Air Clinical Air Clinical Water Clinical Air Clinical Air Clinical Air Clinical Air Clinical Air Clinical Air Clinical Air

2A 10 10 18 18 19 19 25 25 10 10 18 18 19 19 25 25 10 10 18 18 20 20 25 25 10 10 18 18 20 20 25 25 10 10 18 18 20 20 25 25 10 10 18 18 20 20 25 25 10 10 18 18 21 21 25 25 10 10 18 18 21 21 25 25 10 10 18 18 21 21 25 25 10 10 18 18 21 21 25 25 10 10 18 18 21 21 26 26 10 10

2B 14 14 12 12 22 22 19 19 14 14 12 12 25 25 20 20 14 14 12 12 17 17 20 20 15 15 12 12 19 19 20 20 16 16 12 12 19 19 20 20 16 16 12 12 19 19 20 20 16 16 12 12 22 22 21 21 16 16 12 12 22 22 22 22 16 16 12 12 25 25 22 22 16 16 12 12 25 25 26 26 16 16 12 12 25 25 20 20 16 16

2C 10 10 11 11 21 21 19 19 10 10 11 11 34 34 11 11 10 10 13 13 16 16 13 13 10 10 14 14 15 15 8 8 10 10 14 14 15 15 8 8 10 10 16 16 8 8 9 9 10 10 17 17 18 18 8 8 10 10 8 8 18 18 19 19 10 10 8 8 18 18 20 20 10 10 8 8 19 19 9 9 10 10 8 8 19 19 8 8 10 10

3A 17 17 16 16 34 34 26 26 17 17 26 26 34 34 10 10 17 17 14 14 39 39 37 37 18 18 14 14 39 39 10 10 17 17 27 27 40 40 10 10 22 22 26 26 31 31 10 10 23 23 25 25 26 26 29 29 24 24 27 27 26 26 28 28 25 25 27 27 27 27 27 27 25 25 28 28 27 27 10 10 26 26 28 28 27 27 25 25 30 30

3B 13 13 10 10 10 10 19 19 13 13 11 11 23 23 9 9 13 13 10 10 11 11 9 9 12 12 14 14 12 12 10 10 13 13 11 11 12 12 10 10 12 12 11 11 14 14 10 10 13 13 10 10 10 10 9 9 11 11 10 10 10 10 9 9 11 11 10 10 12 12 9 9 12 12 10 10 12 12 10 10 12 12 10 10 12 12 9 9 13 13

3C 14 14 13 13 29 29 17 17 14 14 20 20 26 26 7 7 15 15 12 12 22 22 10 10 12 12 14 14 7 7 21 21 19 19 14 14 7 7 22 22 12 12 20 20 20 20 7 7 21 21 21 21 14 14 6 6 8 8 19 19 15 15 26 26 8 8 20 20 7 7 26 26 8 8 20 20 7 7 7 7 8 8 21 21 7 7 7 7 21 21

4A 7 7 8 8 14 14 10 10 7 7 8 8 10 10 8 8 7 7 8 8 12 12 8 8 7 7 19 19 10 10 9 9 7 7 9 9 10 10 9 9 7 7 8 8 9 9 8 8 7 7 8 8 9 9 8 8 7 7 9 9 9 9 10 10 7 7 9 9 20.3 20.3 10 10 7 7 9 9 20.3 20.3 9 9 7 7 9 9 21 21 8 8 7 7

4B 5 5 9 9 9 9 16 16 5 5 8 8 10 10 10 10 5 5 9 9 11 11 10 10 5 5 10 10 11 11 10 10 5 5 11 11 11 11 10 10 5 5 8 8 9 9 10 10 5 5 9 9 13 13 10 10 5 5 9 9 13 13 9 9 5 5 9 9 10 10 9 9 5 5 9 9 10 10 9 9 5 5 9 9 10 10 10 10 5 5

4C 5 5 5 5 7 7 8 8 6 6 5 5 5 5 20 20 5 5 5 5 8 8 8 8 6 6 5 5 12 12 5 5 6 6 7 7 12 12 5 5 5 5 7 7 5 5 10 10 6 6 7 7 8 8 20 20 5 5 5 5 8 8 5 5 6 6 5 5 8 8 5 5 6 6 5 5 8 8 5 5 6 6 5 5 8 8 10 10 5 5

No. Matches 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2

Label A A AA AA AAA AAA AAAA AAAA B B BB BB BBB BBB BBBB BBBB C C CC CC CCC CCC CCCC CCCC D D DD DD DDD DDD DDDD DDDD E E EE EE EEE EEE EEEE EEEE F F FF FF FFF FFF FFFF FFFF G G GG GG GGG GGG GGGG GGGG H H HH HH HHH HHH HHHH HHHH I I II II III III IIII IIII J J JJ JJ JJJ JJJ JJJJ JJJJ K K KK KK KKK KKK KKKK KKKK L L

730 178 1089 369 1317 518 557 44 816 1474 1101 375 575 1706 836 1748 1117 388 588 1407 843 244 1125 394 593 1410 819 224 1130 1548 600 1708 824 228 1136 405 622 1417 830 1742 1150 1549 646 1427 853 1749 1153 411 640 118 872 1751 1154 415 1350 1658 876 1498 1177 433 666 1720 924 1511 1199 444 667 136 932 1755 1216 1691 668 1722 943 295 1381 1695 670 1723 944 297 1242 476 687 147 956 310 1250 1700

Clinical Air Clinical Air Clinical Air Clinical Air Clinical Env Clinical Air Clinical Water Clinical Water Clinical Air Clinical Env Clinical Air Clinical Air Clinical Env Clinical Air Clinical Env Clinical Water Clinical Air Clinical Air Clinical Env Clinical Water Clinical Env Clinical Env Clinical Water Clinical Air Clinical Air Clinical Water Clinical Air Clinical Soil Clinical Env Clinical Air Clinical Water Clinical Env Clinical Air Clinical Air Clinical Water Clinical Soil Clinical Water Clinical Air Clinical Soil Clinical Water Clinical Air Clinical Air Clinical Air Clinical Air Clinical Soil

18 18 22 22 26 26 10 10 18 18 23 23 11 11 18 18 23 23 11 11 18 18 23 23 13 13 18 18 23 23 13 13 18 18 23 23 14 14 18 18 23 23 14 14 18 18 23 23 14 14 18 18 23 23 14 14 18 18 23 23 15 15 18 18 23 23 15 15 18 18 23 23 15 15 19 19 25 25 15 15 19 19 25 25 17 17 19 19 25 25

12 12 19 19 20 20 16 16 17 17 16 16 12 12 19 19 19 19 14 14 19 19 19 19 10 10 19 19 19 19 19 19 19 19 19 19 12 12 19 19 19 19 20 20 20 20 19 19 20 20 21 21 19 19 20 20 21 21 21 21 19 19 25 25 23 23 19 19 28 28 24 24 19 19 12 12 10 10 19 19 12 12 16 16 12 12 22 22 19 19

8 8 15 15 8 8 10 10 16 16 8 8 17 17 11 11 15 15 14 14 11 11 15 15 9 9 8 8 15 15 8 8 8 8 15 15 9 9 8 8 16 16 11 11 9 9 16 16 8 8 19 19 16 16 9 9 27 27 8 8 8 8 19 19 15 15 8 8 8 8 15 15 8 8 12 12 8 8 9 9 15 15 23 23 13 13 21 21 16 16

31 31 37 37 35 35 31 31 36 36 56 56 25 25 27 27 47 47 27 27 27 27 48 48 10 10 10 10 49 49 22 22 25 25 50 50 26 26 28 28 29 29 34 34 10 10 30 30 36 36 22 22 44 44 31 31 62 62 48 48 26 26 28 28 38 38 33 33 16 16 48 48 34 34 25 25 86 86 10 10 17 17 22 22 16 16 33 33 26 26

10 10 11 11 9 9 13 13 21 21 10 10 22 22 10 10 11 11 11 11 10 10 11 11 11 11 10 10 11 11 10 10 23 23 11 11 10 10 14 14 17 17 9 9 10 10 17 17 13 13 11 11 20 20 9 9 11 11 9 9 10 10 11 11 11 11 15 15 10 10 13 13 15 15 25 25 9 9 10 10 25 25 11 11 10 10 10 10 13 13

20 20 21 21 7 7 21 21 24 24 20 20 21 21 34 34 7 7 5 5 35 35 7 7 9 9 20 20 7 7 10 10 20 20 7 7 20 20 21 21 7 7 7 7 12 12 7 7 10 10 31 31 7 7 10 10 30 30 6 6 7 7 7 7 49 49 20 20 18 18 7 7 20 20 35 35 12 12 13 13 12 12 20 20 22 22 29 29 7 7

9 9 10 10 8 8 7 7 15.3 15.3 12.3 12.3 14 14 20 20 13 13 15 15 20 20 13 13 8 8 9 9 13 13 9 9 15 15 13 13 8 8 9 9 10 10 8 8 8 8 10 10 8 8 10 10 13.3 13.3 8 8 17.3 17.3 8 8 8 8 17.3 17.3 10 10 9 9 8 8 10 10 9 9 12 12 8 8 9 9 16 16 12 12 8 8 14 14 10 10

9 9 26 26 10 10 5 5 9 9 10 10 8 8 11 11 9 9 8 8 11 11 9 9 9 9 9 9 9 9 10 10 9 9 9 9 8 8 9 9 26 26 10 10 10 10 26 26 10 10 8 8 9 9 10 10 9 9 9 9 9 9 10 10 26 26 10 10 9 9 9 9 10 10 12 12 7 7 10 10 10 10 11 11 8 8 9 9 16 16

5 5 5 5 20 20 5 5 8 8 8 8 5 5 5 5 5 5 7 7 5 5 5 5 19 19 10 10 5 5 21 21 5 5 5 5 10 10 5 5 5 5 12 12 5 5 5 5 5 5 8 8 7 7 28 28 5 5 5 5 5 5 8 8 8 8 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 8 8 8 8 7 7 8 8

0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2

LL LL LLL LLL LLLL LLLL M M MM MM MMM MMM N N NN NN NNN NNN O O OO OO OOO OOO P P PP PP PPP PPP Q Q QQ QQ QQQ QQQ R R RR RR RRR RRR S S SS SS SSS SSS T T TT TT TTT TTT U U UU UU UUU UUU V V VV VV VVV VVV W W WW WW WWW WWW X X XX XX XXX XXX Y Y YY YY YYY YYY Z Z ZZ ZZ ZZZ ZZZ