UMD2.0 UMD2.1 UMD2.3 UMD2.4 UMD2.5 [Info] AssemblyDate 2008_? 2009_0122 2009_0210 2009_0217 2009_0312 WgsVersion 4.? 5.2 5.2 5.2 5.2 QualitylessReads no no yes yes yes 1000+Libraries/SomeBadQlessReads no yes yes no no ContaminantReads yes yes yes yes "no" [Scaffolds] TotalScaffolds 134612 66141 56891 45826 39978 TotalContigsInScaffolds 194643 120461 122851 96562 90135 MeanContigsPerScaffold 1.45 1.82 2.16 2.11 2.25 MinContigsPerScaffold 1 1 1 1 1 MaxContigsPerScaffold 258 457 679 587 545 TotalBasesInScaffolds 2858277365 2702609713 2697514858 2685338130 2676390147 MeanBasesInScaffolds 21233 40861 47415 58599 66947 MinBasesInScaffolds 205 432 407 385 316 MaxBasesInScaffolds 14616007 26048998 31687363 33910139 33907885 N25ScaffoldBases 4049462 7892915 9527628 12864407 12846854 N50ScaffoldBases 2055041 4340953 4639522 6999206 8179794 N75ScaffoldBases 661293 1925651 2009237 3128328 3527955 ScaffoldAt1000000000 3128828 6115710 6905906 9740086 10230430 ScaffoldAt2000000000 956250 2037084 2098013 3221207 3605077 TotalSpanOfScaffolds 3000296203 2822470272 2893044516 2732740274 2723015757 MeanSpanOfScaffolds 22288 42674 50852 59633 68113 MinScaffoldSpan 205 432 407 385 316 MaxScaffoldSpan 15072136 26554268 33122578 34283622 34162356 IntraScaffoldGaps 60031 54320 65960 50736 50157 2KbScaffolds 31576 12057 13135 8977 8667 2KbScaffoldSpan 2861613899 2751036688 2835232498 2684248342 2681796012 MeanSequenceGapLength 2366 2207 2964 934 930 [Top5Scaffolds=contigs,size,span,avgContig,avgGap] 0 258,14616007,15072136,56651,1775 457,26048998,26554268,57000,1108 679,31687363,33122578,46668,2117 550,33910139,34283622,61655,680 545,33907885,34162356,62216,468 1 222,10218752,10405580,46030,845 407,21750714,21944974,53442,478 444,21485963,22432826,48392,2137 587,30874011,30991740,52596,201 477,31650686,31952653,66354,634 2 195,9891927,10403240,50728,2636 355,21066634,21546874,59343,1357 536,19273865,20188689,35959,1710 424,25646533,25989906,60487,812 506,26948945,27134821,53259,368 3 205,9852145,10300284,48059,2197 297,17242334,17864991,58055,2104 404,19227595,19946474,47593,1784 371,25177138,25527676,67863,947 446,24729146,24905414,55447,396 4 162,9703963,9850776,59901,912 330,17088677,17407470,51784,969 459,19224258,19657351,41883,946 362,23195922,23758345,64077,1558 413,24609018,25074193,59586,1129 total 1042,54282794,56032016,52095,1687 1846,103197357,105318577,55903,1152 2522,110899044,115347918,43973,1768 2294,138803743,140551289,60507,763 2387,141845680,143229437,59424,581 [Contigs] TotalContigsInScaffolds 194643 120461 122851 96562 90135 TotalBasesInScaffolds 2858277365 2702609713 2697514858 2685338130 2676390147 TotalVarRecords 2618164 2506487 2555630 2668779 2670071 MeanContigLength 14685 22436 21958 27809 29693 MinContigLength 73 65 64 65 65 MaxContigLength 742802 627911 651167 739442 1160130 N25ContigBases 138066 149660 128541 165905 170219 N50ContigBases 74604 85030 71561 94021 95988 N75ContigBases 32524 41862 35271 47780 48606 ContigAt1000000000 107377 113260 96250 124736 126181 ContigAt2000000000 40157 43342 36439 48555 49096 [BigContigs_greater_10000] TotalBigContigs 45939 42352 48038 39567 39111 BigContigLength 2546781351 2536133665 2517018851 2556707724 2556239604 MeanBigContigLength 55438 59882 52396 64617 65359 MinBigContig 10000 10000 10002 10000 10000 MaxBigContig 742802 627911 651167 739442 1160130 BigContigsPercentBases 89.10 93.84 93.31 95.21 95.51 [SmallContigs] TotalSmallContigs 148704 78109 74813 56995 51024 SmallContigLength 311496014 166476048 180496007 128630406 120150543 MeanSmallContigLength 2095 2131 2413 2257 2355 MinSmallContig 73 65 64 65 65 MaxSmallContig 9999 9999 9999 9999 9999 SmallContigsPercentBases 10.90 6.16 6.69 4.79 4.49 [DegenContigs] TotalDegenContigs 425095 269031 268237 253847 251413 DegenContigLength 416917446 270824509 273575106 254620227 252279234 MeanDegenContigLength 981 1007 1020 1003 1003 MinDegenContig 70 65 65 65 65 MaxDegenContig 21929 33824 30246 39964 39964 DegenPercentBases 14.59 10.02 10.14 9.48 9.43 [Top5Contigs=reads,bases] 0 10137,742802 18122,627911 20738,651167 23367,739442 37335,1160130 1 15463,725518 6725,606674 17623,608563 13617,730446 34273,988622 2 12724,706032 5933,604149 15505,591937 13980,723911 36188,953379 3 6945,661067 7082,594326 10751,577861 30729,707043 38312,784188 4 18030,631769 10466,592012 6243,573088 22083,665772 15249,746877 total 63299,3467188 48328,3025072 70860,3002616 103776,3566614 161357,4633196 [UniqueUnitigs] TotalUUnitigs 2145703 1125858 1268177 1361335 1345585 MinUUnitigLength 69 64 64 21 21 MaxUUnitigLength 78607 161926 139524 139508 139508 MeanUUnitigLength 1881 2937 2673 2544 2563 SDUUnitigLength 2852 5873 5589 5401 5503 [Surrogates] TotalSurrogates 265756 92943 95651 92634 92035 SurrogateInstances 282756 97109 101836 97514 96711 SurrogateLength 320310608 113174176 119233845 110866311 109579684 SurrogateInstanceLength 355694318 123235054 133381069 121888106 120041802 UnPlacedSurrReadLen 570006088 291995468 299513607 239333170 231446437 PlacedSurrReadLen 602293115 184492030 231989631 223950966 220533764 MinSurrogateLength 71 66 66 66 66 MaxSurrogateLength 23963 73289 73300 73296 73296 MeanSurrogateLength 1205 1218 1247 1197 1191 SDSurrogateLength 716 876 955 908 889 [Mates] ReadsWithNoMate 2177410(6.18%)8711921(24.94%) 2478705(6.97%) 2479621(6.98%) 2484136(7.00%) ReadsWithGoodMate 25205306(71.5%)20676328(59.2%)26284142(73.9%)27239776(76.6%)27263138(76.8%) ReadsWithBadShortMate 3986(0.01%) 276928(0.79%) 477738(1.34%) 5148(0.01%) 5784(0.02%) ReadsWithBadLongMate 69042(0.20%) 46392(0.13%) 125012(0.35%) 76666(0.22%) 76640(0.22%) ReadsWithSameOrientMate 59054(0.17%) 44902(0.13%) 92064(0.26%) 96268(0.27%) 96862(0.27%) ReadsWithOuttieMate 30062(0.09%) 17502(0.05%) 47240(0.13%) 41198(0.12%) 41142(0.12%) ReadsWithBothChaffMate 1815854(5.15%) 2320274(6.64%) 2460166(6.92%) 2472550(6.96%) 2467462(6.95%) ReadsWithChaffMate 2548258(7.23%) 1391964(3.99%) 1615110(4.54%) 1483194(4.17%) 1465034(4.13%) ReadsWithBothDegenMate 867888(2.46%) 436396(1.25%) 540580(1.52%) 473294(1.33%) 465114(1.31%) ReadsWithDegenMate 516438(1.47%) 236464(0.68%) 375166(1.06%) 223030(0.63%) 213768(0.60%) ReadsWithBothSurrMate 11740(0.03%) 1178(0.00%) 2736(0.01%) 3300(0.01%) 3278(0.01%) ReadsWithSurrogateMate 1525430(4.33%) 466302(1.34%) 613670(1.73%) 567616(1.60%) 555510(1.56%) ReadsWithDiffScafMate 407400(1.16%) 300846(0.86%) 437990(1.23%) 386200(1.09%) 369294(1.04%) ReadsWithUnassignedMate 0(0.00%) 0(0.00%) 0(0.00%) 0(0.00%) 0(0.00%) TotalScaffoldLinks 832 711 2807 533 474 MeanScaffoldLinkWeight 6.04 12.91 5.39 7.04 6.36 [Reads] TotalReadsInput NA NA NA 35547861 NA TotalUsableReads 35237868 34927397 35550319 35547861 35507162 AvgClearRange 778 800 799 794 794 ContigReads 29419293(83.5%)29778572(85.3%)30359479(85.4%)30613401(86.1%)30609464(86.2%) BigContigReads 28183374(78.0%)28872361(82.7%)29329656(82.5%)29928249(84.2%)29952842(84.4%) SmallContigReads 1235919(3.51%) 906211(2.59%) 1029823(2.90%) 685152(1.93%) 656622(1.85%) DegenContigReads 1516126(4.30%) 1074367(3.08%) 1116879(3.14%) 992408(2.79%) 979728(2.76%) SurrogateReads 1418376(4.03%) 574657(1.65%) 643165(1.81%) 562272(1.58%) 548545(1.54%) PlacedSurrogateReads 718121(2.04%) 221322(0.63%) 277831(0.78%) 268984(0.76%) 264880(0.75%) SingletonReads 3602194(10.22%)3721123(10.65%)3708627(10.43%)3648764(10.26%)3634305(10.24%) ChaffReads 3602082(10.22%)3721105(10.65%)3701713(10.41%)3648744(10.26%)3634031(10.23%) [Coverage] ContigsOnly 8.23 8.88 9.06 9.12 9.15 Contigs_Surrogates 8.43 8.99 9.18 9.21 9.23 Contigs_Degens_Surrogates 7.73 8.48 8.65 8.70 8.72 AllReads 9.59 10.34 10.54 10.51 10.53 [TotalBaseCounts] BasesCount NA NA NA 35321443284 NA ClearRangeLengthFRG NA NA NA 29285951589 NA ClearRangeLengthASM 27406137041 27943626590 28420422997 28227984641 28195475059 SurrogateBaseLength 1172299203 476487498 531503238 463284136 451980201 ContigBaseLength 23511603264 24010874849 24452314327 24486604612 24480763831 DegenBaseLength 1229108706 909505020 943927527 840661049 830698073 SingletonBaseLength 2095418983 2731251253 2724667536 2661385810 2652566718 Contig_SurrBaseLength 24081609352 24302870317 24751827934 24725937782 24712210268 [gcContent] Content 42.13 41.54 41.53 41.54 41.53