S1 E1 S2 E2 Reference Contig IDY Ambiguous Best_group 405587 448751 43139 1 NC_007795.1 scf1 99.9 True relocation, inconsistency = -5297 400861 405756 53172 48267 NC_007795.1 scf1 99.82 True fake: scaffold gap size wrong estimation (local) 391954 399362 61843 54481 NC_007795.1 scf1 99.36 True local misassembly 387100 391788 66518 61844 NC_007795.1 scf1 99.47 True local misassembly 336945 386957 116463 66519 NC_007795.1 scf1 99.84 True fake: scaffold gap size wrong estimation (local) 293848 336799 159384 116564 NC_007795.1 scf1 99.65 True fake: scaffold gap size wrong estimation (local) 291593 291694 161350 161249 NC_007795.1 scf1 95.1 True local misassembly 290842 290922 161571 161491 NC_007795.1 scf1 95.06 True fake: scaffold gap size wrong estimation (local) 290122 290609 162257 161770 NC_007795.1 scf1 99.18 True fake: scaffold gap size wrong estimation (extensive) 289575 289829 164136 163882 NC_007795.1 scf1 95.69 True indel: indel (<= 5bp) 289485 289569 164221 164137 NC_007795.1 scf1 96.47 True relocation, inconsistency = -1022 289813 289913 164915 164815 NC_007795.1 scf1 98.02 True fake: scaffold gap size wrong estimation (extensive) 289813 290612 166494 165695 NC_007795.1 scf1 96.25 True fake: scaffold gap size wrong estimation (local) 282001 289555 174246 166692 NC_007795.1 scf1 99.99 True local misassembly 265263 281843 190793 174247 NC_007795.1 scf1 99.77 True fake: scaffold gap size wrong estimation (local) 264652 265256 191953 191349 NC_007795.1 scf1 99.83 True fake: scaffold gap size wrong estimation (local) 116114 264271 340198 192341 NC_007795.1 scf1 99.76 True fake: scaffold gap size wrong estimation (local) 104531 115380 351435 340751 NC_007795.1 scf1 98.45 True local misassembly 57254 104416 398444 351436 NC_007795.1 scf1 99.64 True fake: scaffold gap size wrong estimation (extensive) 34152 56066 422664 400735 NC_007795.1 scf1 99.88 True relocation, scaffold gap is present, inconsistency = -53519 24286 34154 486024 476181 NC_007795.1 scf1 99.73 True local misassembly 1 24153 510178 486032 NC_007795.1 scf1 99.94 True fake: not a misassembly [linear representation of circular genome] 2812518 2821361 519009 510179 NC_007795.1 scf1 99.84 True fake: scaffold gap size wrong estimation (local) 2811375 2812188 520514 519701 NC_007795.1 scf1 100.0 True fake: scaffold gap size wrong estimation (local) 2723923 2810784 607755 521043 NC_007795.1 scf1 99.75 True fake: scaffold gap size wrong estimation (local) 2633028 2723297 698468 608331 NC_007795.1 scf1 99.81 True local misassembly 2613567 2632868 717769 698469 NC_007795.1 scf1 99.97 True local misassembly 2581951 2613405 749155 717783 NC_007795.1 scf1 99.69 True fake: scaffold gap size wrong estimation (local) 2578407 2581727 752602 749282 NC_007795.1 scf1 100.0 True local misassembly 2573502 2578219 757357 752641 NC_007795.1 scf1 99.83 True fake: scaffold gap size wrong estimation (extensive) 2571184 2571463 758415 758136 NC_007795.1 scf1 99.64 True fake: scaffold gap size wrong estimation (local) 2526000 2570809 803571 758812 NC_007795.1 scf1 99.83 True local misassembly 2487075 2525890 842359 803572 NC_007795.1 scf1 99.91 True local misassembly 2425940 2486883 903147 842360 NC_007795.1 scf1 99.64 True fake: scaffold gap size wrong estimation (local) 2399404 2425287 929522 903638 NC_007795.1 scf1 99.98 True local misassembly 2395338 2399103 933290 929523 NC_007795.1 scf1 99.95 True local misassembly 2378423 2395234 950089 933291 NC_007795.1 scf1 99.88 True local misassembly 2346132 2378246 982153 950090 NC_007795.1 scf1 99.81 True local misassembly 2335895 2345969 992228 982154 NC_007795.1 scf1 99.89 True local misassembly 2265983 2335779 1061967 992229 NC_007795.1 scf1 99.89 True fake: scaffold gap size wrong estimation (local) 2256232 2264611 1072046 1063643 NC_007795.1 scf1 99.98 True local misassembly 2244368 2256114 1083792 1072047 NC_007795.1 scf1 99.91 True CONTIG scf1 1083792 misassembled 1865413 1897298 31886 1 NC_007795.1 scf2 99.98 True fake: scaffold gap size wrong estimation (local) 1845095 1864529 52032 32608 NC_007795.1 scf2 99.91 True fake: scaffold gap size wrong estimation (local) 1842064 1844475 54834 52405 NC_007795.1 scf2 99.96 True fake: scaffold gap size wrong estimation (local) 1832805 1840575 63884 56114 NC_007795.1 scf2 99.95 True local misassembly 1821384 1832614 75106 63885 NC_007795.1 scf2 99.9 True fake: scaffold gap size wrong estimation (local) 1815361 1820825 80973 75509 NC_007795.1 scf2 99.98 True fake: scaffold gap size wrong estimation (local) 1802212 1813690 93925 82489 NC_007795.1 scf2 99.59 True fake: scaffold gap size wrong estimation (local) 1796319 1802150 100106 94261 NC_007795.1 scf2 99.98 True fake: scaffold gap size wrong estimation (local) 1776873 1795541 119339 100702 NC_007795.1 scf2 99.8 True fake: scaffold gap size wrong estimation (local) 1760881 1775915 135043 120042 NC_007795.1 scf2 99.77 True local misassembly 1719052 1760721 176542 135044 NC_007795.1 scf2 99.53 True fake: scaffold gap size wrong estimation (local) 1707574 1718992 188127 176704 NC_007795.1 scf2 99.98 True fake: scaffold gap size wrong estimation (local) 1670728 1705749 224624 189733 NC_007795.1 scf2 99.61 True local misassembly 1655267 1670603 239924 224625 NC_007795.1 scf2 99.76 True fake: scaffold gap size wrong estimation (local) 1641451 1654945 253606 240115 NC_007795.1 scf2 99.96 True local misassembly 1597823 1641282 297047 253607 NC_007795.1 scf2 99.93 True local misassembly 1511226 1597680 383388 297048 NC_007795.1 scf2 99.83 True local misassembly 1506385 1511085 388094 383395 NC_007795.1 scf2 98.96 True fake: scaffold gap size wrong estimation (local) 1502423 1502828 391100 390695 NC_007795.1 scf2 96.06 True relocation, inconsistency = -458400 1960276 1960789 391650 391134 NC_007795.1 scf2 95.94 True relocation, inconsistency = 457837 1496394 1501853 397694 392236 NC_007795.1 scf2 96.7 True relocation, scaffold gap is present, inconsistency = -564662 2059838 2060421 398912 398329 NC_007795.1 scf2 95.72 True relocation, inconsistency = 564887 1493517 1493923 400346 399940 NC_007795.1 scf2 97.3 True local misassembly 1464425 1493483 429589 400616 NC_007795.1 scf2 97.28 True local misassembly 1461015 1462574 433683 432137 NC_007795.1 scf2 99.17 True local misassembly 1386868 1460835 507530 433684 NC_007795.1 scf2 99.81 True relocation, inconsistency = -3174 1384897 1386881 512675 510691 NC_007795.1 scf2 100.0 True local misassembly 1381953 1384910 515712 512755 NC_007795.1 scf2 99.97 True local misassembly 1378292 1381574 518975 515713 NC_007795.1 scf2 98.93 True local misassembly 1375355 1378060 521681 518976 NC_007795.1 scf2 99.34 True local misassembly 1363070 1375221 533824 521683 NC_007795.1 scf2 99.88 True fake: scaffold gap size wrong estimation (local) 1349747 1362963 547683 534467 NC_007795.1 scf2 99.98 True local misassembly 1333104 1349615 564153 547684 NC_007795.1 scf2 99.73 True fake: scaffold gap size wrong estimation (local) 1286762 1332663 610307 564446 NC_007795.1 scf2 99.86 True local misassembly 1250594 1286600 646314 610308 NC_007795.1 scf2 99.98 True fake: scaffold gap size wrong estimation (local) 1248957 1250522 648427 646862 NC_007795.1 scf2 99.94 True local misassembly 1192029 1248843 705122 648431 NC_007795.1 scf2 99.77 True local misassembly 1111448 1191888 785436 705123 NC_007795.1 scf2 99.76 True fake: scaffold gap size wrong estimation (local) 1074622 1111137 822051 785626 NC_007795.1 scf2 99.72 True local misassembly 1022757 1074452 873736 822052 NC_007795.1 scf2 99.96 True local misassembly 1004124 1022611 892224 873737 NC_007795.1 scf2 99.97 True local misassembly 978244 1003967 917827 892225 NC_007795.1 scf2 99.51 True local misassembly 937125 978076 958690 917828 NC_007795.1 scf2 99.75 True local misassembly 917320 936975 978286 958691 NC_007795.1 scf2 99.67 True fake: scaffold gap size wrong estimation (local) 860531 916970 1034883 978504 NC_007795.1 scf2 99.87 True local misassembly 820970 860411 1074207 1034884 NC_007795.1 scf2 99.64 True fake: scaffold gap size wrong estimation (local) 815656 820999 1080293 1074943 NC_007795.1 scf2 99.87 True relocation, inconsistency = -13781 811804 815672 1097926 1094058 NC_007795.1 scf2 99.97 True fake: scaffold gap size wrong estimation (local) 776069 811600 1133469 1097952 NC_007795.1 scf2 99.82 True fake: scaffold gap size wrong estimation (local) 768605 775705 1140896 1133796 NC_007795.1 scf2 99.92 True fake: scaffold gap size wrong estimation (local) 758678 768182 1150496 1141055 NC_007795.1 scf2 99.32 True relocation, inconsistency = 1199 746490 757478 1161485 1150497 NC_007795.1 scf2 100.0 True local misassembly 721085 746494 1187245 1161964 NC_007795.1 scf2 99.42 True local misassembly 665245 720892 1242821 1187258 NC_007795.1 scf2 99.75 True fake: scaffold gap size wrong estimation (local) 632186 665256 1276248 1243240 NC_007795.1 scf2 99.79 True local misassembly 624380 632052 1283910 1276249 NC_007795.1 scf2 99.83 True local misassembly 613168 623980 1294714 1283911 NC_007795.1 scf2 99.52 True relocation, inconsistency = -13303 554984 613170 1366179 1308015 NC_007795.1 scf2 99.75 True fake: scaffold gap size wrong estimation (local) 554053 554199 1366923 1366777 NC_007795.1 scf2 97.96 True fake: scaffold gap size wrong estimation (extensive) 550274 554203 1374441 1370584 NC_007795.1 scf2 97.94 True local misassembly 550043 550160 1374560 1374443 NC_007795.1 scf2 100.0 True indel: stretch of mismatches 498311 550037 1426293 1374566 NC_007795.1 scf2 99.98 True CONTIG scf2 1426293 misassembled 2201737 2237254 35491 1 NC_007795.1 scf3 99.66 True fake: scaffold gap size wrong estimation (local) 2194493 2201280 42600 35813 NC_007795.1 scf3 100.0 True local misassembly 2128190 2194358 108825 42601 NC_007795.1 scf3 99.89 True CONTIG scf3 108825 correct 1906498 1909726 1 3193 NC_007795.1 scf4 98.79 True local misassembly 1909853 1923397 3194 16742 NC_007795.1 scf4 99.97 True relocation, inconsistency = 43615 1967013 2018230 16743 67845 NC_007795.1 scf4 99.41 True fake: scaffold gap size wrong estimation (local) 2018594 2043611 68062 93015 NC_007795.1 scf4 99.42 True fake: scaffold gap size wrong estimation (extensive) 2059079 2059450 107385 107756 NC_007795.1 scf4 97.85 True local misassembly 2061920 2062169 110150 110399 NC_007795.1 scf4 98.4 True local misassembly 2067879 2068420 116993 117534 NC_007795.1 scf4 95.2 True fake: scaffold gap size wrong estimation (local) 2069446 2069895 117810 118259 NC_007795.1 scf4 98.44 True relocation, scaffold gap is present, inconsistency = -567507 1503547 1506424 119418 122294 NC_007795.1 scf4 99.51 True relocation, inconsistency = 566182 2073485 2119608 123173 169172 NC_007795.1 scf4 99.67 True local misassembly 2119719 2122744 169173 172198 NC_007795.1 scf4 99.97 True CONTIG scf4 172198 misassembled 454278 492188 1 37884 NC_007795.1 scf5 99.89 True CONTIG scf5 37884 correct 1820754 1821206 465 1 NC_007795.1 scf6 96.78 True CONTIG scf6 465 correct CONTIG 14 1412 unaligned CONTIG 228 2085 unaligned CONTIG 4 3417 unaligned CONTIG 421 3285 unaligned CONTIG 431 6926 unaligned 2237165 2238611 1447 1 NC_007795.1 507 99.93 True CONTIG 507 1447 correct CONTIG 606 1032 unaligned CONTIG 607 7404 unaligned 2239250 2242351 1 3102 NC_007795.1 617 100.0 True CONTIG 617 3102 correct 492994 494884 1875 1 NC_007795.1 620 99.1 True CONTIG 620 1875 correct 399473 400960 1488 1 NC_007795.1 621 99.87 True CONTIG 621 1488 correct