Bm.qc combine: Difference between revisions
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MaxScaffoldSpan 6532311 23313 2323624 1788901 | MaxScaffoldSpan 6532311 23313 2323624 1788901 | ||
IntraScaffoldGaps 3478 107 2511 3353 | IntraScaffoldGaps 3478 107 2511 3353 | ||
N25ScaffoldBases NA 1753 129247 472523 | N25ScaffoldBases NA 1753 129247 472523 | ||
N75ScaffoldBases NA 1109 14222 18959 | N75ScaffoldBases NA 1109 14222 18959 | ||
2KbScaffolds NA 131 3701 3193 | 2KbScaffolds NA 131 3701 3193 | ||
2KbScaffoldSpan NA 663003 78716002 84858641 | 2KbScaffoldSpan NA 663003 78716002 84858641 | ||
MeanSequenceGapLength | MeanSequenceGapLength 1961 2295 2167 2926 | ||
[Top5Scaffolds=contigs,size,span,avgContig,avgGap] | [Top5Scaffolds=contigs,size,span,avgContig,avgGap] | ||
| Line 45: | Line 43: | ||
TotalContigsInScaffolds 11714 1513 12659 13607 | TotalContigsInScaffolds 11714 1513 12659 13607 | ||
TotalBasesInScaffolds 70676234 1980831 82012118 84309668 | TotalBasesInScaffolds 70676234 1980831 82012118 84309668 | ||
N50ContigBases 25236 1257 27474 30726 | N50ContigBases 25236 1257 27474 30726 | ||
TotalVarRecords NA 1953 86085 145646 | TotalVarRecords NA 1953 86085 145646 | ||
MeanContigLength | MeanContigLength 6033 1309 6479 6196 | ||
MinContigLength | MinContigLength 206 280 274 66 | ||
MaxContigLength | MaxContigLength 611010 4952 565900 522243 | ||
N25ContigBases NA 1527 65357 101916 | N25ContigBases NA 1527 65357 101916 | ||
N50ContigBases 25236 1257 27474 30726 | |||
N75ContigBases NA 1097 6100 5654 | N75ContigBases NA 1097 6100 5654 | ||
| Line 59: | Line 55: | ||
TotalBigContigs 1208 0 1609 1417 | TotalBigContigs 1208 0 1609 1417 | ||
BigContigLength 46649303 0 57310605 58560900 | BigContigLength 46649303 0 57310605 58560900 | ||
MinBigContig 10018 0 10014 10024 | MinBigContig 10018 0 10014 10024 | ||
MaxBigContig 611010 0 565900 522243 | MaxBigContig 611010 0 565900 522243 | ||
BigContigsPercentBases 66.00 0.00 69.88 69.46 | BigContigsPercentBases 66.00 0.00 69.88 69.46 | ||
MeanBigContigLength | MeanBigContigLength 38616 0 35619 41327 | ||
[SmallContigs] | [SmallContigs] | ||
| Line 77: | Line 72: | ||
TotalDegenContigs 18868 192840 8497 114780 | TotalDegenContigs 18868 192840 8497 114780 | ||
DegenContigLength 17526009 56098824 10297846 42193843 | DegenContigLength 17526009 56098824 10297846 42193843 | ||
MinDegenContig 71 63 65 63 | MinDegenContig 71 63 65 63 | ||
MaxDegenContig 54918 5688 82776 25405 | MaxDegenContig 54918 5688 82776 25405 | ||
DegenPercentBases 24.80 2832.09 12.56 50.05 | DegenPercentBases 24.80 2832.09 12.56 50.05 | ||
DegenVarRecords NA 66751 10425 57124 | DegenVarRecords NA 66751 10425 57124 | ||
MeanDegenContigLength | MeanDegenContigLength 928 291 1212 368 | ||
[Top5Contigs=reads,bases,EUID] | [Top5Contigs=reads,bases,EUID] | ||
| Line 93: | Line 87: | ||
[Surrogates] | [Surrogates] | ||
TotalSurrogates NA 20 5856 6785 | TotalSurrogates NA 20 5856 6785 | ||
SurrogateInstances NA 20 7225 8483 | SurrogateInstances NA 20 7225 8483 | ||
| Line 102: | Line 92: | ||
SurrogateInstanceLength NA 8388 25015803 15522342 | SurrogateInstanceLength NA 8388 25015803 15522342 | ||
UnPlacedSurrReadLen NA 81891 239498624 120812859 | UnPlacedSurrReadLen NA 81891 239498624 120812859 | ||
PlacedSurrReadLen NA 1170 37248682 33034388 | PlacedSurrReadLen NA 1170 37248682 33034388 | ||
MinSurrogateLength | MinSurrogateLength 140 96 161 65 | ||
MaxSurrogateLength | MaxSurrogateLength 67942 1285 90056 58392 | ||
MeanSurrogateLength | MeanSurrogateLength 2063 424 2936 1457 | ||
SDSurrogateLength | SDSurrogateLength 3010 262 6189 2509 | ||
[Mates] | [Mates] | ||
Latest revision as of 16:08, 1 March 2010
boost2 454 Sanger hybrid [Info] assemblyDate ? 02/24/10 2/24/10 2/24/10 inputReads Sanger(all) 454 Sanger(filt) 454+Sanger(filt) wgsVersion ? 6.0-beta 6.0-beta 6.0-beta unitigger utg? bog bog bog ovlOverlapper ovl? mer mer mer obtMerThreshold ? 200 200 400 ovlMerThreshold ? 60 60 120 aStat boostLargeCtgEndSurrogates default default default [Scaffolds] TotalScaffolds 8236 1406 10148 10254 TotalContigsInScaffolds 11714 1513 12659 13607 MeanContigsPerScaffold 1.42 1.08 1.25 1.33 MinContigsPerScaffold 1 1 1 1 MaxContigsPerScaffold 188 5 40 48 TotalBasesInScaffolds 70676234 1980831 82012118 84309668 MeanBasesInScaffolds 8581.38 1409 8082 8222 MinBasesInScaffolds 778 585 904 283 MaxBasesInScaffolds 6421643 7572 2307981 1721555 N50ScaffoldBases 93771 1289 46197 117198 TotalSpanOfScaffolds 77496734 2226417 87454189 94122201 MeanSpanOfScaffolds 9409.51 1584 8618 9179 MinScaffoldSpan 778 585 904 283 MaxScaffoldSpan 6532311 23313 2323624 1788901 IntraScaffoldGaps 3478 107 2511 3353 N25ScaffoldBases NA 1753 129247 472523 N75ScaffoldBases NA 1109 14222 18959 2KbScaffolds NA 131 3701 3193 2KbScaffoldSpan NA 663003 78716002 84858641 MeanSequenceGapLength 1961 2295 2167 2926 [Top5Scaffolds=contigs,size,span,avgContig,avgGap] 0 188,6421643,6532311,34157,591 4,7572,7789,1893,72 40,2307981,2323624,57700,401 48,1721555,1788901,35866,1433 1 57,3798332,3953718,66637,2774 5,6479,8696,1296,554 24,1516999,1532321,63208,666 15,1185197,1203477,79013,1306 2 34,3329997,3480804,97941,4569 2,6083,6694,3042,611 23,1340524,1356064,58284,706 11,1108784,1129504,100799,2072 3 97,3001588,3057655,30944,584 4,5906,8258,1476,784 15,1140592,1149533,76039,639 14,1079545,1092527,77110,999 4 18,1841703,1968674,102316,7468 4,5514,8532,1378,1006 25,1070426,1081655,42817,468 17,1022143,1026496,60126,272 total 394,18393263,18993162,46683,1542 19,31554,39969,1661,601 127,7376522,7443197,58083,547 105,6117224,6240905,58259,1237 [Contigs] TotalContigsInScaffolds 11714 1513 12659 13607 TotalBasesInScaffolds 70676234 1980831 82012118 84309668 N50ContigBases 25236 1257 27474 30726 TotalVarRecords NA 1953 86085 145646 MeanContigLength 6033 1309 6479 6196 MinContigLength 206 280 274 66 MaxContigLength 611010 4952 565900 522243 N25ContigBases NA 1527 65357 101916 N50ContigBases 25236 1257 27474 30726 N75ContigBases NA 1097 6100 5654 [BigContigs_greater_10000] TotalBigContigs 1208 0 1609 1417 BigContigLength 46649303 0 57310605 58560900 MinBigContig 10018 0 10014 10024 MaxBigContig 611010 0 565900 522243 BigContigsPercentBases 66.00 0.00 69.88 69.46 MeanBigContigLength 38616 0 35619 41327 [SmallContigs] TotalSmallContigs 10506 1513 11050 12190 SmallContigLength 24026931 1980831 24701513 25748768 MeanSmallContigSize 2286.97 NA NA NA MinSmallContig 206 280 274 66 MaxSmallContig 9993 4952 9968 9975 SmallContigsPercentBases 34.00 100.00 30.12 30.54 MeanSmallContigLength NA 1309 2235 2112 [DegenContigs] TotalDegenContigs 18868 192840 8497 114780 DegenContigLength 17526009 56098824 10297846 42193843 MinDegenContig 71 63 65 63 MaxDegenContig 54918 5688 82776 25405 DegenPercentBases 24.80 2832.09 12.56 50.05 DegenVarRecords NA 66751 10425 57124 MeanDegenContigLength 928 291 1212 368 [Top5Contigs=reads,bases,EUID] 0 11363,611010 227,4952 7237,565900 17214,522243 1 10025,523376 113,4737 4447,351060 18092,508032 2 8614,412675 327,4094 4699,331465 8957,400176 3 7453,409597 210,3799 3610,306648 13159,379926 4 6001,383913 105,3688 4775,301942 12954,379724 total 43456,2340571 982,21270 24768,1857015 70376,2190101 [Surrogates] TotalSurrogates NA 20 5856 6785 SurrogateInstances NA 20 7225 8483 SurrogateLength NA 8484 17192360 9886209 SurrogateInstanceLength NA 8388 25015803 15522342 UnPlacedSurrReadLen NA 81891 239498624 120812859 PlacedSurrReadLen NA 1170 37248682 33034388 MinSurrogateLength 140 96 161 65 MaxSurrogateLength 67942 1285 90056 58392 MeanSurrogateLength 2063 424 2936 1457 SDSurrogateLength 3010 262 6189 2509 [Mates] ReadsWithNoMate 1011672197998(83.93%) 117707(10.03%)2347967(60.99%) ReadsWithBadMate 2388 NA NA NA ReadsWithGoodMate 524910 1044(0.04%) 465244(39.65%) 806560(20.95%) ReadsWithUnusedMate 604540 NA NA NA TotalScaffoldLinks 87 4 116 387 MeanScaffoldLinkWeight 4.46 2.50 3.50 8.70 ReadsWithBadShortMate NA 158(0.01%) 1760(0.15%) 2092(0.05%) ReadsWithBadLongMate NA 8(0.00%) 1036(0.09%) 2488(0.06%) ReadsWithSameOrientMate NA 86(0.00%) 910(0.08%) 5592(0.15%) ReadsWithOuttieMate NA 72(0.00%) 368(0.03%) 1772(0.05%) ReadsWithBothChaffMate NA 27690(1.06%) 53194(4.53%) 48840(1.27%) ReadsWithChaffMate NA 100682(3.84%) 36650(3.12%) 104996(2.73%) ReadsWithBothDegenMate NA 279388(10.67%) 199770(17.03%) 213034(5.53%) ReadsWithDegenMate NA 11342(0.43%) 51246(4.37%) 90260(2.34%) ReadsWithBothSurrMate NA 0(0.00%) 416(0.04%) 110(0.00%) ReadsWithSurrogateMate NA 24(0.00%) 226444(19.30%) 174634(4.54%) ReadsWithDiffScafMate NA 348(0.01%) 18596(1.58%) 51496(1.34%) ReadsWithUnassignedMate NA 0(0.00%) 0(0.00%) 0(0.00%) [Reads] TotalReadsInput 1233005 3297077 1178192 4475269 ContigReads 784696(63.64%) 47342(1.81%) 678087(57.79%)1657932(43.06%) BigContigReads 648924(52.62%) 0(0.00%) 559113(47.65%)1407760(36.57%) SmallContigReads 135772(11.01%) 47342(1.81%) 118974(10.14%) 250172(6.50%) DegenContigReads 132616(10.75%)1530785(58.45%) 109437(9.33%)1052007(27.33%) SurrogateReads 139594(11.32%) 376(0.01%) 342175(29.16%) 281402(7.31%) SingletonReads 176099(14.28%)1040349(39.73%) 89055(7.59%) 904884(23.50%) TotalUsableReads NA 2618840 1173341 3849841 AvgClearRange NA 235 791 410 PlacedSurrogateReads NA 12(0.00%) 45413(3.87%) 46384(1.20%) ChaffReads NA1039561(39.70%) 89048(7.59%) 904272(23.49%) [Coverage] ContigsOnly 9.61 5.46 6.62 10.91 ContigsAndDegens 10.94 NA NA NA AllReads 12.47 310.18 11.32 18.73 Contigs_Surrogates NA 5.50 9.54 12.35 Contigs_Degens_Surrogates NA 6.20 9.41 10.46 [gcContent] Content 0.30 32.70 30.11 29.99 [UniqueUnitigs] TotalUUnitigs NA 1534 26192 36145 MinUUnitigLength NA 72 64 64 MaxUUnitigLength NA 4155 307689 132923 MeanUUnitigLength NA 1301 2774 2515 SDUUnitigLength NA 394 6807 5214 [TotalBaseCounts] BasesCount NA NA NA NA ClearRangeLengthFRG NA NA NA NA ClearRangeLengthASM NA 614416134 927974911 1579010968 SurrogateBaseLength NA 83061 276747306 153847247 ContigBaseLength NA 10821164 542975021 920163174 DegenBaseLength NA 349180617 86620911 282002680 SingletonBaseLength NA 254332462 58880355 256032255 Contig_SurrBaseLength NA 10903055 782473645 1040976033 [Unitig Consensus] NumColumnsInUnitigs NA 938983681 476792687 1197917290 NumGapsInUnitigs NA 2374725 1486629 4486947 NumRunsOfGapsInUnitigReads NA 37987307 20659878 90359012 [Contig Consensus] NumColumnsInUnitigs NA 58875009 92725198 127951717 NumGapsInUnitigs NA 795848 417174 1450876 NumRunsOfGapsInUnitigReads NA 13186973 4439224 28262805 NumColumnsInContigs NA 58856256 92705330 127898545 NumGapsInContigs NA 776491 395785 1395140 NumRunsOfGapsInContigReads NA 12345375 4187916 26412719 NumAAMismatches NA 75765 148474 294243 NumVARStringsWithFlankingGaps NA 8689 23928 42375