Bm.qc combine

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                                   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