No. words: 68081; after pruning: 57930 Histogram of relative pair offsets, for read pairs with multiple alignments: 1 2 19 2 56 4 58 2 59 2 76 2 80 2 81 2 99 312 Pass 1 Gap Score Merge:(0) 0 0.0 19.2 (1,1:1008) 643 3.49 3.05 0.55 djs228_2390.s1 40 956 (111) C djs228_2933.s1 (95) 981 42 * Merge:(0) 0 0.0 17.3 (2,1:814) 579 3.14 1.09 2.54 djs228_2933.s1 210 1036 (40) djs228_2751.s1 20 834 (371) * Merge:(0) 0 0.0 17.2 (1,1:58) 657 1.61 1.61 0.12 djs228_1331.s1 88 892 (136) djs228_2664.s1 28 844 (0) * Merge:(0) 0 0.0 16.8 (1,1:46) 665 1.94 0.13 0.13 djs228_2714.s1 78 849 (0) djs228_891.s1 32 803 (503) * Merge:(0) 0 0.0 16.8 (1,1:966) 628 5.69 0.83 0.59 djs228_1343.s1 84 927 (157) C djs228_539.s1 (62) 884 39 * Merge:(0) 1 0.0 16.3 (1,1:804) 694 0.27 0.00 0.00 djs228_2222.s1 35 769 (265) C djs228_2282.s1 (121) 771 37 * Merge:(0) 0 0.0 16.2 (2,1:866) 656 1.17 0.26 0.39 djs228_2714.s1 36 801 (48) C djs228_2346.s1 (224) 831 67 * Merge:(0) 0 0.0 15.7 (1,1:-75) 627 0.69 0.00 1.39 djs228_1033.s1 31 750 (69) djs228_433.s1 107 816 (289) * Merge:(0) 0 0.0 15.7 (3,3:1331) 423 8.25 3.00 1.00 djs228_2390.s1 157 956 (111) C djs228_891.s1 (171) 1135 320 * Merge:(0) 0 0.0 15.6 (1,1:170) 604 2.36 1.67 0.00 djs228_2862.s1 210 928 (83) djs228_560.s1 38 768 (30) * Merge:(0) 0 0.0 15.4 (1,1:138) 576 6.43 0.00 0.40 djs228_1680.s1 172 917 (140) djs228_2912.s1 34 776 (284) * Merge:(0) 0 0.0 15.3 (2,1:972) 550 6.35 0.41 0.41 djs228_560.s1 38 777 (21) C djs228_2632.s1 (50) 765 26 * Merge:(0) 0 0.0 15.2 (1,1:1044) 504 4.97 0.27 3.09 djs228_1029.s1 83 826 (0) C djs228_2417.s1 (553) 943 221 * Merge:(0) 0 0.0 15.1 (2,2:-345) 637 1.73 0.14 0.29 djs228_1343.s1 37 728 (356) djs228_2912.s1 245 935 (125) * Merge:(0) 0 0.0 15.1 (2,2:556) 633 1.16 0.29 0.00 djs228_2282.s1 202 890 (2) djs228_433.s1 28 718 (387) * Merge:(0) 0 0.0 15.1 (4,2:-582) 545 7.53 0.13 0.40 djs228_1680.s1 41 784 (273) C djs228_2417.s1 (730) 766 25 * Merge:(0) 0 0.0 14.7 (2,1:111) 606 0.75 0.00 0.00 djs228_1331.s1 148 817 (211) djs228_331.s1 37 706 (6) * Merge:(0) 0 0.0 14.4 (4,1:632) 613 0.76 0.00 0.00 djs228_433.s1 28 682 (423) djs228_441.s3 29 683 (0) * Merge:(0) 0 0.0 14.3 (1,1:24) 613 0.77 0.00 0.00 djs228_1211.s1 62 708 (91) djs228_1740.s1 38 684 (243) * Merge:(0) 0 0.0 13.5 (6,1:734) 550 1.92 0.16 0.80 djs228_1343.s1 72 697 (387) C djs228_1418.s1 (3) 660 39 * Merge:(0) 0 0.0 13.5 (1,1:-160) 452 6.03 0.00 1.96 djs228_168.s1 141 803 (57) djs228_2436.s1 303 952 (552) * Merge:(0) 0 0.0 13.4 (2,1:72) 576 0.33 0.00 0.33 djs228_1740.s1 76 684 (243) djs228_1919.s1 28 634 (527) * Merge:(0) 0 0.0 13.4 (5,3:-593) 519 3.82 0.16 0.32 djs228_1033.s1 189 816 (3) C djs228_560.s1 (6) 792 166 * Merge:(0) 0 0.0 13.1 (1,1:793) 610 1.95 0.28 0.56 djs228_2151.s1 40 757 (378) C djs228_671.s2 (342) 754 39 * Merge:(0) 0 0.0 12.6 (1,1:205) 544 1.04 0.00 0.17 djs228_1034.s1 244 819 (0) djs228_1422.s1 39 613 (52) * Merge:(0) 0 0.0 12.5 (1,1:881) 454 2.32 2.32 0.17 djs228_1051.s1 209 812 (0) C djs228_2116.s1 (441) 686 70 * Merge:(0) 0 0.0 12.3 (7,1:1172) 523 1.94 0.00 0.00 djs228_539.s1 38 604 (342) djs228_1013.s1 244 810 (3) * Merge:(0) 0 0.0 12.1 (2,1:80) 473 0.36 0.00 1.08 djs228_1051.s1 118 670 (142) djs228_523.s1 38 584 (247) * Merge:(0) 0 0.0 11.7 (8,1:32) 525 0.54 0.36 0.00 djs228_2862.s1 37 592 (419) C djs228_3196.s1 (193) 591 34 * Merge:(0) 0 0.0 11.1 (3,3:577) 439 1.77 0.00 0.00 djs228_1051.s1 35 543 (269) C djs228_1331.s1 (484) 544 36 * Merge:(0) 0 0.0 11.1 (1,1:-123) 392 3.37 0.37 3.00 djs228_1153.s1 334 867 (502) djs228_2019.s1 459 978 (189) * Merge:(0) 0 0.0 11.0 (3,2:1040) 496 2.05 0.32 2.37 djs228_1740.s1 52 684 (243) C djs228_1153.s1 (416) 953 334 * Merge:(0) 0 0.0 10.4 (6,1:1071) 250 18.32 0.52 0.17 djs228_2116.s1 36 608 (519) djs228_1777.s1 226 800 (350) * Merge:(0) 0 0.0 9.7 (8,2:677) 421 1.59 0.00 1.79 djs228_1013.s1 29 532 (281) djs228_671.s2 328 822 (274) * Merge:(0) 0 0.0 9.1 (6,1:730) 318 11.19 0.90 0.36 djs228_2751.s1 262 815 (390) djs228_1141.s1 177 733 (485) * Merge:(0) 0 0.0 9.0 (10,7:-192) 350 5.05 0.00 2.11 djs228_1029.s1 31 505 (321) djs228_2751.s1 458 922 (283) Merge:(0) 0 0.0 8.8 (7,5:141) 371 1.18 0.24 0.24 djs228_2664.s1 412 833 (11) djs228_1211.s1 33 454 (345) * Merge:(0) 0 0.0 8.6 (9,1:48) 377 1.21 0.24 0.00 djs228_2862.s1 195 606 (405) C djs228_1929.s1 (933) 448 36 * Merge:(0) 0 0.0 8.0 (17,12:2129) 253 5.91 0.00 1.54 djs228_2151.s1 419 807 (328) djs228_1777.s1 38 420 (730) * Merge:(0) 0 0.0 7.7 (2,1:486) 327 1.42 0.57 0.00 djs228_1422.s1 313 663 (2) djs228_1094.s1 31 383 (432) * Merge:(0) 0 0.0 7.5 (10,2:736) 274 5.31 0.84 0.00 djs228_2222.s1 614 971 (63) djs228_2436.s1 37 397 (1107) * Merge:(0) 0 0.0 6.1 (29,1:2400) 274 0.00 0.00 0.00 djs228_2019.s1 459 734 (433) C djs228_2529.s2 (477) 294 19 * Merge:(0) 0 0.0 6.0 (3,1:12) 246 0.37 0.00 0.00 djs228_1034.s1 49 319 (500) djs228_2273.s1 37 307 (591) * Merge:(0) 0 0.0 5.3 (12,1:350) 285 7.71 0.93 0.00 djs228_2436.s1 37 464 (1040) djs228_474.s2 261 692 (542) * Merge:(0) 0 0.0 5.3 (13,4:-460) 180 7.31 0.77 0.38 djs228_3196.s1 525 784 (0) djs228_1034.s1 32 292 (527) * Merge:(0) 0 -0.7 4.2 (17,1:361) 138 14.66 0.38 0.38 djs228_474.s2 325 590 (644) djs228_426.s1 313 578 (820) Merge:(0) 0 0.0 4.0 (30,1:2482) 180 0.00 0.00 0.00 djs228_1740.s1 503 684 (243) djs228_2338.s1 33 214 (759) * Merge:(0) 0 0.0 3.4 (31,1:1468) 135 0.00 0.00 0.00 djs228_671.s2 39 192 (904) djs228_671.s1 37 190 (0) * Pass: 1 #reads #contigs (not counting singlets) 1 17 18 1 32 1 N.B. Following not based on all pairs!! Lowest # merges # failures LLR score 0.0 47 0 -0.7 1 0 Gap # merges # failures size 0 47 0 1 1 0 Offset 0 75 1 64 2 33 3 14 4 6 5 2 7 1 8 1 14 2 Pass 3 Gap Score Merge:(0) 0 0.0 16.5 (32,1:-1693) 620 5.07 1.80 0.23 djs228_2346.s1 89 975 (80) C djs228_715.s1 (6) 957 57 * Merge:(0) 0 0.0 15.0 (18,1:-1699) 638 1.31 0.00 0.15 djs228_1094.s1 31 715 (100) C djs228_2854.s1 (269) 723 40 * Merge:(0) 0 0.0 9.1 (19,1:1119) 333 1.85 3.70 0.00 djs228_168.s1 423 854 (6) djs228_2813.s1 37 484 (1071) * Merge:(0) 0 0.0 5.8 (33,1:2368) 271 0.00 1.38 0.00 djs228_2019.s1 459 748 (419) C djs228_1803.s1 (948) 326 33 * Merge:(0) 0 0.0 4.8 (20,1:102) 167 17.42 0.68 0.68 djs228_2282.s1 161 602 (290) C djs228_844.s1 (933) 542 101 Pass: 3 #reads #contigs (not counting singlets) 1 12 21 1 34 1 N.B. Following not based on all pairs!! Lowest # merges # failures LLR score 0.0 5 0 Gap # merges # failures size 0 5 0 Offset 0 8 1 6 2 5 3 5 4 1 Pass 4 Gap Score Merge:(0) 0 0.0 11.7 (21,1:636) 188 20.15 1.63 1.04 djs228_433.s1 43 717 (388) djs228_481.s2 47 725 (571) Merge:(0) 0 0.0 10.4 (34,1:-713) 211 15.36 2.50 0.71 djs228_1029.s1 31 590 (236) djs228_1273.s1 159 728 (102) Merge:(0) 0 -1.3 9.1 (35,1:2068) 209 17.67 0.60 0.20 djs228_1153.s1 336 833 (536) C djs228_2083.s1 (542) 626 127 Merge:(0) 0 0.0 8.3 (36,1:-730) 126 20.67 1.25 1.25 djs228_2751.s1 325 803 (402) djs228_3085.s1 49 527 (348) Merge:(0) 0 0.0 5.5 (22,1:922) 110 19.55 0.64 0.00 djs228_168.s1 209 520 (340) djs228_1248.s1 21 334 (388) Merge:(0) 0 0.0 4.7 (23,1:339) 93 19.16 0.38 0.00 djs228_2436.s1 64 324 (1180) djs228_434.s3 301 562 (149) Merge:(0) 0 0.0 4.4 (37,24:-3536) 104 6.11 0.87 6.55 djs228_715.s1 50 278 (685) djs228_2813.s1 779 994 (561) Merge:(0) 0 0.0 4.0 (61,1:-4971) 86 6.57 4.55 2.02 djs228_1034.s1 168 365 (454) C djs228_2078.s1 (378) 808 606 Merge:(0) 0 -2.0 3.0 (62,1:3367) 111 6.62 0.00 1.32 djs228_2529.s2 144 294 (477) C djs228_2659.s1 (2) 824 676 Merge:(0) 0 0.0 3.0 (63,1:-3969) 48 20.23 1.73 0.58 djs228_433.s1 518 690 (415) C djs228_2949.s1 (688) 547 373 Merge:(0) 0 0.0 2.8 (64,1:3517) 68 4.51 9.02 0.00 djs228_1153.s1 334 466 (903) djs228_1336.s1 819 963 (192) Merge:(0) 0 0.0 1.1 (65,1:-3436) 42 5.36 1.79 0.00 djs228_844.s1 539 594 (881) djs228_892.s1 540 596 (563) * Merge:(0) 0 0.0 0.8 (66,1:751) 30 7.69 0.00 0.00 djs228_539.s1 136 174 (772) C djs228_2894.s1 (1250) 81 43 Pass: 4 #reads #contigs (not counting singlets) 67 1 N.B. Following not based on all pairs!! Lowest # merges # failures LLR score 0.0 11 0 -1.3 1 0 -2.0 1 0 Gap # merges # failures size 0 13 0 Offset 0 20 1 20 2 19 3 10 4 1 6 1 18 1 19 2 20 2 21 1 Read equivalence class histogram: 67 1 Chimera merges: Contig 1: 35440 nodes 5288 str. conn. components Path 1 djs228_2854.s1 1 51 C djs228_1094.s1 704 63 djs228_2854.s1 63 78 C djs228_1094.s1 677 90 djs228_2854.s1 90 108 C djs228_1094.s1 647 124 djs228_2854.s1 124 216 C djs228_1094.s1 539 308 djs228_2854.s1 308 478 C djs228_1094.s1 277 497 C djs228_1034.s1 745 774 djs228_2854.s1 774 802 C djs228_1034.s1 440 835 djs228_2854.s1 834 839 C djs228_1034.s1 403 963 djs228_2078.s1 698 964 C djs228_1034.s1 278 995 djs228_2078.s1 729 1004 C djs228_2273.s1 226 1015 djs228_2078.s1 751 1019 C djs228_2273.s1 211 1048 djs228_2078.s1 783 1053 C djs228_2273.s1 177 1116 C djs228_1034.s1 126 1156 C djs228_3196.s1 579 1203 C djs228_1034.s1 39 1207 djs228_2862.s1 99 1266 C djs228_3196.s1 469 1537 C djs228_1033.s1 725 1561 djs228_2862.s1 452 1776 djs228_2222.s1 70 1898 C djs228_1033.s1 364 1906 djs228_2222.s1 200 1908 C djs228_2282.s1 604 1910 djs228_560.s1 630 1929 C djs228_441.s3 410 1952 djs228_560.s1 672 1963 djs228_844.s1 154 1981 C djs228_441.s3 358 2107 C djs228_433.s1 231 2280 C djs228_481.s2 62 2292 C djs228_2282.s1 220 2318 djs228_474.s2 259 2337 djs228_2436.s1 54 2626 djs228_474.s2 570 2630 djs228_2436.s1 347 2774 djs228_168.s1 329 2975 djs228_2813.s1 144 3203 djs228_1248.s1 572 3207 djs228_2813.s1 376 3224 djs228_168.s1 775 3228 djs228_2813.s1 397 3251 djs228_168.s1 799 3255 djs228_2813.s1 424 3613 djs228_715.s1 53 3699 C djs228_2346.s1 898 3707 djs228_715.s1 147 3733 C djs228_2346.s1 864 3745 djs228_715.s1 185 3755 C djs228_2346.s1 842 3788 djs228_2714.s1 58 3792 C djs228_2346.s1 805 3808 djs228_2714.s1 78 3827 C djs228_2346.s1 770 3843 djs228_891.s1 67 3900 djs228_2714.s1 170 4255 djs228_2933.s1 201 4305 djs228_891.s1 529 4309 djs228_2714.s1 579 4311 C djs228_2390.s1 750 4315 djs228_2714.s1 585 4371 C djs228_2390.s1 690 4378 djs228_2751.s1 134 4513 C djs228_2390.s1 548 4805 djs228_1029.s1 134 4806 djs228_2933.s1 753 4815 C djs228_2390.s1 246 4865 djs228_2751.s1 621 4870 djs228_1029.s1 199 4897 C djs228_2390.s1 164 4906 C djs228_2417.s1 808 4908 djs228_1029.s1 237 4913 djs228_2933.s1 874 4917 djs228_1029.s1 246 4923 djs228_1141.s1 594 4926 djs228_2751.s1 680 4966 djs228_1680.s1 57 5021 djs228_2751.s1 775 5030 C djs228_2417.s1 687 5047 djs228_1680.s1 137 5088 C djs228_2417.s1 631 5112 djs228_2912.s1 64 5123 C djs228_2417.s1 596 5160 djs228_1029.s1 489 5394 djs228_1680.s1 484 5558 djs228_1343.s1 302 5609 C djs228_2417.s1 110 5667 djs228_1343.s1 411 5773 C djs228_1418.s1 219 5949 C djs228_671.s2 778 5961 djs228_1343.s1 705 5964 C djs228_539.s1 260 5996 C djs228_1013.s1 434 6156 C djs228_539.s1 68 6172 C djs228_1013.s1 258 6391 djs228_1777.s1 75 6421 djs228_2151.s1 486 6466 C djs228_671.s2 263 6538 djs228_2151.s1 603 6593 C djs228_671.s2 136 6595 C djs228_671.s1 132 6601 C djs228_671.s2 128 6660 C djs228_1051.s1 728 6668 djs228_1777.s1 352 6672 C djs228_671.s2 57 6677 C djs228_671.s1 50 6679 C djs228_1051.s1 709 6689 djs228_2116.s1 183 6742 djs228_1777.s1 426 6744 C djs228_1051.s1 644 6749 djs228_2116.s1 243 6869 C djs228_1051.s1 519 6870 C djs228_523.s1 438 7266 djs228_331.s1 346 7465 C djs228_1153.s1 825 7485 djs228_1211.s1 238 7531 C djs228_1153.s1 759 7563 djs228_1211.s1 316 7579 C djs228_1153.s1 711 7592 C djs228_2019.s1 823 7596 C djs228_1153.s1 694 7598 C djs228_2019.s1 817 7602 C djs228_1153.s1 688 7631 C djs228_2019.s1 784 Contig length: old 8938, new 8414 Badly positioned read start: djs228_1153.s1, 6906 - 6928 Badly positioned read start: djs228_2417.s1, 4200 - 4227 Contig length: old 8414, new 7915 New start: 39 S Change at: 3104; seg lengths: entry 2, contig 2 D Change at: 3503; seg lengths: entry 4, contig 6 S Change at: 6149; seg lengths: entry 1, contig 1 S Change at: 6654; seg lengths: entry 1, contig 1 Contig 1 unpadded => padded conversion: 200 => 200 400 => 400 600 => 601 800 => 802 1000 => 1012 1200 => 1215 1400 => 1417 1600 => 1618 1800 => 1829 2000 => 2031 2200 => 2240 2400 => 2447 2600 => 2648 2800 => 2851 3000 => 3052 3200 => 3253 3400 => 3453 3600 => 3655 3800 => 3860 4000 => 4060 4200 => 4260 4200 => 4261 4400 => 4465 4600 => 4674 4800 => 4895 5000 => 5118 5200 => 5327 5400 => 5528 5600 => 5734 5800 => 5937 6000 => 6139 6200 => 6340 6400 => 6540 6600 => 6741 6800 => 6948 7000 => 7150 7200 => 7369 7400 => 7572 7600 => 7777 7800 => 8003 7800 => 8004