Spreadsheet: c205bb53-f0fb-483d-aa0f-385a0e2b1fd2
Sheet: Table S1

Supplementary Table 1
(A)
Biological Replicate |  | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | Total
Sample Name |  | GM10860 | GM17106 | GM17189 | GM17207 | GM17220 | GM17253 | GM10860 | GM17106 | GM17189 | GM17207 | GM17220 | GM17253
Total number of reads |  | 5710459 | 4521161 | 9042976 | 8248565 | 5309473 | 6115782 | 5558002 | 5131706 | 6413744 | 6106569 | 7002028 | 7478815
[NAME] |  | 2455540 | 2855914 | 5691058 | 4816073 | 3289887 | 3726517 | 2858700 | 2990306 | 3939424 | 3389198 | 4127429 | 4465642
 | Both [NAME] | 1288384 | 1311894 | 2792427 | 2292982 | 1594065 | 1844143 | 1480215 | 1405227 | 1898983 | 1638017 | 2019486 | 2298682
 | One Mate Unique | 408467 | 548976 | 1072336 | 918472 | 621054 | 695882 | 537989 | 576249 | 763958 | 649784 | 773042 | 830555
 | Both [NAME] | 758689 | 995044 | 1826295 | 1604619 | 1074768 | 1186492 | 840496 | 1008830 | 1276483 | 1101397 | 1334901 | 1336405
[NAME] on + Strand |  | 1396737 | 1628157 | 3210261 | 2753544 | 1872510 | 2125213 | 1624301 | 1709356 | 2246480 | 1922537 | 2340270 | 2536355
[NAME] on - Strand |  | 1058803 | 1227757 | 2480797 | 2062529 | 1417377 | 1601304 | 1234399 | 1280950 | 1692944 | 1466661 | 1787159 | 1929287
(B)
 | Filters |  |  |  | Tag clusters |  |  | Reads
 | Has peak within 40bp | Precision 3'end > other | Less than 10 A's in 20bp | Count > 8 per sample | Count | Count in polyAdb2 | % in polyAdb2 | Count | Count in polyAdb2 | % in polyAdb2
 | Pass | Pass | Pass | Pass | 18714 | 12119 | 0.6476088698904622 | 34286211 | 24111639 | 0.7032459492243106
 | Pass | Pass | Pass | Fail | 21122 | 4541 | 0.2149891108796516 | 860826 | 221914 | 0.2577919347231613
 | Pass | Pass | Fail | Pass | 4866 | 468 | 0.09617755856966707 | 3356226 | 358316 | 0.1067615828016349
 | Pass | Pass | Fail | Fail | 15534 | 336 | 0.0216299729625338 | 576798 | 15396 | 0.02669218686611257
 | Pass | Fail | Pass | Pass | 10 | 2 | 0.2 | 1343 | 136 | 0.1012658227848101
 | Pass | Fail | Pass | Fail | 589 | 75 | 0.1273344651952462 | 15646 | 2004 | 0.1280838552984788
 | Pass | Fail | Fail | Pass | 3 | 0 | 0 | 364 | 0 | 0
 | Pass | Fail | Fail | Fail | 202 | 2 | 0.009900990099009901 | 5136 | 60 | 0.01168224299065421
 | Fail | Pass | Pass | Pass | 2874 | 614 | 0.2136395267919276 | 1934464 | 651458 | 0.336764085555482
 | Fail | Pass | Pass | Fail | 4905 | 378 | 0.07706422018348624 | 212877 | 18208 | 0.08553296034799439
 | Fail | Pass | Fail | Pass | 940 | 209 | 0.2223404255319149 | 1340569 | 425294 | 0.3172488696963752
 | Fail | Pass | Fail | Fail | 835 | 44 | 0.05269461077844311 | 36310 | 2182 | 0.06009363811622143
 | Fail | Fail | Pass | Pass | 36 | 0 | 0 | 24508 | 0 | 0
 | Fail | Fail | Pass | Fail | 118 | 9 | 0.07627118644067797 | 4250 | 321 | 0.07552941176470589
 | Fail | Fail | Fail | Pass | 3 | 0 | 0 | 578 | 0 | 0
 | Fail | Fail | Fail | Fail | 32 | 0 | 0 | 1017 | 0 | 0
 | Total |  |  |  | 70784 | 18798 | 0.2655684900542495 | 42657123 | 25806928 | 0.6049851979000084
(C)
 | Feature | Reads |  | Tag clusters
 |  | Count | Proportion | Count | Proportion | Count in polyAdb2 | % in polyAdb2
 | Coding 3' UTR | 27822346 |  | 12985 |  | 10287
 | Coding Other | 520112 |  | 1441 |  | 372
 | Noncoding Last Exon | 1558238 |  | 782 |  | 461
 | Noncoding Other | 136635 |  | 273 |  | 88
 | Within 1kb | 284029 |  | 449 |  | 230
 | Unannotated | 1566226 |  | 2758 |  | 681
 | Total without chrM | 31887586 |  | 18688 |  | 12119
 | chrM | 2398540 |  | 26
 | Total | 34286126 |  | 18714