Spreadsheet: 01c4ef55-13c2-4e0d-b6ac-dcf7bac1dd7c
Sheet: S1

Table S1. Comparison of SNP calls to those by [NAME] et al., Nature, 2012.
 | Called by [NAME] et al |  | Called in this study
Line | A Number of variants | B Number of SNPs   not within 30 bps of non-SNPs | C Number of variants * | D Number of SNPs   not within 30 bps of non-SNPs | Number of exact matches A - C | Number of variants in A overlapping with variants in C | Number of variants in C overlapping with variants in A | % of variants in A matching or overlapping with C | % of variants in C matching or overlapping with A | E Number of Matches B-D | % E / B | % E / D
DGRP-208 | 674529 | 526008 | 803884 | 537115 | 608315 | 30721 | 30701 |  |  | 504170
DGRP-313 | 682811 | 560019 | 799185 | 558343 | 614700 | 22215 | 22205 |  |  | 524701
DGRP-357 | 644350 | 519246 | 778482 | 534097 | 588340 | 22565 | 22551 |  |  | 493898
DGRP-358 | 695893 | 557182 | 824218 | 561152 | 623941 | 26053 | 26037 |  |  | 523399
DGRP-362 | 636822 | 523085 | 778024 | 533455 | 589980 | 19161 | 19159 |  |  | 501943
DGRP-365 | 653202 | 518270 | 787311 | 527522 | 597748 | 26043 | 26032 |  |  | 498368
DGRP-375 | 690425 | 534648 | 807783 | 539596 | 609951 | 33897 | 33871 |  |  | 504335
DGRP-379 | 643914 | 524151 | 782067 | 531512 | 591227 | 21055 | 21054 |  |  | 499758
DGRP-380 | 621890 | 492249 | 789136 | 526246 | 558805 | 25598 | 25587 |  |  | 465076
DGRP-391 | 713986 | 544606 | 820694 | 542413 | 626726 | 37697 | 37662 |  |  | 514643
DGRP-399 | 665942 | 525420 | 788938 | 532501 | 603012 | 28164 | 28152 |  |  | 502294
DGRP-427 | 668815 | 526200 | 790626 | 534873 | 604680 | 29278 | 29260 |  |  | 503895
DGRP-437 | 648714 | 521424 | 777856 | 534775 | 587600 | 24121 | 24111 |  |  | 494122
DGRP-517 | 697413 | 533176 | 812795 | 539433 | 612078 | 35739 | 35654 |  |  | 503946
DGRP-555 | 652500 | 516515 | 791138 | 528673 | 598519 | 25941 | 25937 |  |  | 497631
DGRP-639 | 651471 | 519905 | 784634 | 527397 | 594553 | 23590 | 23581 |  |  | 495139
DGRP-705 | 655525 | 522855 | 791711 | 530762 | 601491 | 23879 | 23874 |  |  | 501200
DGRP-707 | 659053 | 524131 | 784731 | 526560 | 598411 | 25159 | 25156 |  |  | 497935
DGRP-712 | 648559 | 515743 | 776217 | 519923 | 591672 | 23877 | 23874 |  |  | 491687
DGRP-714 | 682961 | 548683 | 790449 | 532311 | 597801 | 24586 | 24583 |  |  | 498515
DGRP-730 | 587647 | 499944 | 781998 | 525963 | 551972 | 14687 | 14687 |  |  | 483263
DGRP-732 | 753488 | 621934 | 783219 | 532585 | 592463 | 23293 | 23285 |  |  | 496622
DGRP-765 | 661473 | 529719 | 780799 | 528274 | 597369 | 23965 | 23959 |  |  | 499507
DGRP-774 | 668519 | 551728 | 738310 | 514534 | 554764 | 21150 | 21148 |  |  | 469506
DGRP-786 | 695426 | 564288 | 809388 | 562267 | 627445 | 24394 | 24390 |  |  | 530674
DGRP-799 | 654378 | 519730 | 778707 | 522690 | 595091 | 24727 | 24724 |  |  | 494845
DGRP-820 | 647010 | 517231 | 786146 | 527882 | 587637 | 22900 | 22899 |  |  | 489285
DGRP-852 | 704502 | 541229 | 821180 | 544534 | 626033 | 35181 | 35136 |  |  | 514962
DGRP-859 | 646352 | 514232 | 773001 | 517186 | 588464 | 23537 | 23535 |  |  | 488820
Total
* excluding chromosome 4 (it is not in the other dataset), and with di-nucleotide substitutions represented as pairs of consecutive SNPs for comparison purposes