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
MeanSequenceGapSize 1961.04 NA NA NA
N25ScaffoldBases NA 1753 129247 472523
N75ScaffoldBases NA 1109 14222 18959
ScaffoldAt1000000 NA 1285 NA NA
2KbScaffolds NA 131 3701 3193
2KbScaffoldSpan NA 663003 78716002 84858641
MeanSequenceGapLength NA 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
MeanContigSize 6033.48 NA NA NA
MinContigSize 206 NA NA NA
MaxContigSize 611010 NA NA NA
N50ContigBases 25236 1257 27474 30726
TotalVarRecords NA 1953 86085 145646
MeanContigLength NA 1309 6479 6196
MinContigLength NA 280 274 66
MaxContigLength NA 4952 565900 522243
N25ContigBases NA 1527 65357 101916
N75ContigBases NA 1097 6100 5654
[BigContigs_greater_10000]
TotalBigContigs 1208 0 1609 1417
BigContigLength 46649303 0 57310605 58560900
MeanBigContigSize 38616.97 NA NA NA
MinBigContig 10018 0 10014 10024
MaxBigContig 611010 0 565900 522243
BigContigsPercentBases 66.00 0.00 69.88 69.46
MeanBigContigLength NA 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
MeanDegenContigSize 928.87 NA NA NA
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 NA 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]
MinSurrogateSize 140 NA NA NA
MaxSurrogateSize 67942 NA NA NA
MeanSurrogateSize 2063.44 NA NA NA
SDSurrogateSize 3010.32 NA NA NA
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 NA 96 161 65
MaxSurrogateLength NA 1285 90056 58392
MeanSurrogateLength NA 424 2936 1457
SDSurrogateLength NA 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