QUAST

Quality Assessment Tool for Genome Assemblies by CAB

Worst Median Best
Genome statisticsABySS_63ABySS_127CLCIDBA_UDMEGAHITmetaVelvetMIRARay_MetaSOAPdenovo2SPAdesSPAdes_metaSPAdes_scSPAdes_sc_carefulVelvetvicunaGeneious
59.04249.15799.71999.64599.73584.59799.6899.64620.48799.73799.73799.62599.71384.59780.94499.741
KC82162599.97810099.873100100-10099.84991.5710010010099.86-75.336100
KC821629100-10010010099.3431001005.08810010010010099.34399.92100
KF302033--98.81298.81298.81298.97998.81298.81212.05698.81298.81298.81298.81298.97998.81298.812
KF302034--99.98199.54699.98199.98199.81699.98112.44599.98199.98199.46699.98199.98191.183100
KF30203599.55899.55899.58499.56799.55899.55899.55899.5583.73399.55899.55899.55899.55699.55899.55899.558
KF302036--98.68698.74498.74489.74398.74498.7446.31898.74498.74498.74498.74489.74354.82498.744
KF302037--98.92598.92598.92598.92598.92598.9256.61598.92598.92598.92598.92598.92551.05498.925
NC_001330100-100100100-10010099.984100100100100-72.187100
NC_00142210095.39510099.6199.424-97.15999.42499.42499.6199.6110099.61-32.88299.61
NC_02179010010010010010099.5461001000.25510010010010099.546100100
NC_02179410010010010010099.4841001007.69310010099.94599.94599.48472.612100
NC_02179610099.97199.9710010099.94610099.40910.73210010010010099.94670.768100
1.0051.0041.0631.0031.0021.0011.071.0141.0191.0021.0011.0021.0011.0011.0821.072
KC82162511.0021.0531.0011.002-1.0971.0010.9991.0011.0031.0041-1.1851.005
KC8216291.024-11.0021.0031.0041.1681.0151.5551.0011.0011.0011.0011.0041.0021.002
KF302033--11.0031.00411.0061.0211.0021.0021.0021.00211.0061.01
KF302034--11.0051.00111.0091.0150.9841.00111.006111.0831.184
KF302035111.97411.00111.34411.7031.0031.00211.00111.0011.002
KF302036--1.0011.0031.00411.0071.0240.9811.0021.0011.0011.00111.2161.01
KF302037--11.0021.00311.0031.0240.9771.0021.0011.0011.00111.161.006
NC_0013301.01-11.0171.023-1.0081.0690.9911.0131.0081.0081.008-1.1821.049
NC_0014221.0111.00411.0051.004-11.0041.0071.0051.0051.0081.013-1.0061.007
NC_0217901.0041.02311.0031.0031.0041.0931.0285.521.0041.0021.0021.0021.0041.0091.436
NC_0217941.001111.0011.00211.0121.0220.9891.0011.0011111.1421.009
NC_0217961111.0011.0021.0021.10410.9971.0021.0011.0011.0011.0021.0571.005
76649766661294151288511295561294781289701290483628112949212947012874812947012947848827129441
KC8216257664976666528917676576807-76666765503628176743769257699376559-157976666
KC82162944392-54016541155415735739359135479921454093540415404254042357394306354016
KF302033--36771368703691236833369903751425136848368263682636826368333699837131
KF302034--12941512885112955612947812897012904897712949212947012874812947012947848827129441
KF30203535176351763517635179351763517770233517635035176351763517635175351773517635176
KF302036--377063782737869207983798138637933378053778337783377832079885138107
KF302037--4455144650446924455844678260641075446284460644606446064455883944829
NC_0013306148-608961886230-6089650860346166613461346134-5606385
NC_00142254455158538653655355-5233535553735365536554314783-7645365
NC_021790385434008939191392903854522872391642305410038545385213852138521228723955239166
NC_02179471499714577144971548715903888071686698258887152671485714107141038880244472069
NC_021796725417251472513726347267636945256977210578470642705987059870598369452341972916
362058301060626708609282610345516986650157616906124681609876609689609027609283516986534402652197
KC8216257664976666806297676576807-84045765507011476743769257699376559-6841076666
KC82162955287-540165411554157538176304754799274854093540415404254042538175397354016
KF302033--367713687036912368333699037514448636848368263682636826368333699837131
KF302034--12941512885112955612947812966213136016037129492129470128748129470129478127741153292
KF3020353517635176489923517935176351774723835176131135176351763517635175351773517635176
KF302036--377063782737869342973798138637236837805377833778337783342972545238107
KF302037--445514465044692445584467845598291044628446064460644606445582665644829
NC_0013306148-608961886230-6089650860346166613461346134-51906385
NC_00142254455158538653655355-5233535553735365536554315410-17715365
NC_021790393134008939191392903932539128428294028110039345392773927739277391283955256245
NC_0217947149971457714497154871590710977228273023543771526714857141071410710975924872069
NC_0217967254172514725137263472676726018008372105776372689726017260172591726015423572916
---7154871590368333916469825-7064270598-7059836833--
KC8216257664976666528917676576807-76666765503383376743769257699376559-67676666
KC82162944392-540165411554157357393591354799-54093540415404254042357394306354016
KF302033--367713687036912368333699037514-36848368263682636826368333699837131
KF302034--129415128851129556129478128970129048-12949212947012874812947012947824884129441
KF3020353517635176-351793517635177277035176-35176351763517635175351773517635176
KF302036--377063782737869207983798138637-378053778337783377832079853538107
KF302037--445514465044692445584467826064-446284460644606446064455852044829
NC_0013306148-608961886230-6089650860346166613461346134-5166385
NC_00142254455158538653655355-5233535553735365536554314783-5065365
NC_0217903854340089391913929038545228723916423054-38545385213852138521228723955239166
NC_0217947149971457714497154871590388807168669825-715267148571410714103888061772069
NC_0217967254172514725137263472676369451744972105-7064270598705987059836945187572916
---3929038545228722569737514-3854538521-3852122872--
KC8216257664976666277387676576807-76666765503383376743769257699376559-58676666
KC82162944392-5401654115541578710231354799-5409354041540425404287104306354016
KF302033--367713687036912368333699037514-36848368263682636826368333699837131
KF302034--129415128851129556129478128970129048-129492129470128748129470129478694129441
KF3020353517635176-351793517635177104535176-35176351763517635175351773517635176
KF302036--37706378273786963593798138637-37805377833778337783635951038107
KF302037--445514465044692445584467819534-446284460644606446064455851044829
NC_0013306148-608961886230-6089650860346166613461346134-5066385
NC_00142254455158538653655355-5233535553735365536554314783-5015365
NC_0217903854340089391913929038545154863916417227-38545385213852138521154863955217079
NC_0217947149971457714497154871590128177168669825-715267148571410714101281752372069
NC_021796725417251472513726347267625815464272105-706427059870598705982581554972916
---44554-44-45--
KC82162511111-1121111-401
KC8216291-111111-1111111
KF302033--111111-1111111
KF302034--111111-1111121
KF30203511-11161-1111111
KF302036--111111-11111211
KF302037--111111-11111231
NC_0013301-111-1111111-51
NC_00142211111-1111111-21
NC_02179011111111-1111111
NC_02179411111111-11111311
NC_02179611111121-1111131
---77997-77-79--
KC82162511211-1121111-671
KC8216291-111251-1111211
KF302033--111111-1111111
KF302034--111111-11111161
KF30203511-111131-1111111
KF302036--111211-11112331
KF302037--111112-11111361
NC_0013301-111-1111111-81
NC_00142211111-1111111-31
NC_02179011111212-1111212
NC_02179411111311-11113571
NC_02179611111241-11112201
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC8216257664976792528917676576807-76720766187644076743769257699376559-65977087
KC82162955287-540165411554157357693591354799-54093540415404254042357694316254124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--12941512951412955612947812965213136011123112949212947012947012947012947824884153292
KF302035351773517635384351813519335177386935176-35292352513517635214351773521435227
KF302036--37728378273786920798379813863736485378053778337783377832079851038107
KF302037--44551446504469244558446784559843295446284460644606446064455850744829
NC_0013306148-608961886230-6135650860346166613461346134-5156385
NC_00142254455158538653915377-5233537753955391539154314809--5402
NC_0217903859340089391913929038545228723918340281-38545385213852138521228723955256262
NC_021794714997145771449715487159038881716867302366950715267148571410714103888157272069
NC_021796725417251472535726347267636945174497210567075706427059870598705983694565672916
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC8216257664976792277387676576807-76720766187644076743769257699376559-55077087
KC82162955287-5401654115541578710511954799-5409354041540425404287104316254124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--129415129514129556129478129652131360111231129492129470129470129470129478690153292
KF302035351773517635384351813519335177259735176-35292352513517635214351773521435227
KF302036--3772837827378694056379813863736485378053778337783377834056-38107
KF302037--445514465044692445584467845598432954462844606446064460644558-44829
NC_0013306148-608961886230-6135650860346166613461346134-5056385
NC_00142254455158538653915377-5233537753955391539154314809--5402
NC_0217903859340089391913929038545155123918340281-38545385213852138521155123955256262
NC_021794714997145771449715487159012817716867302366950715267148571410714101281750872069
NC_0217967254172514725357263472676258151283672105670757064270598705987059825815-72916
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC8216257664976666528917676576807-76666765503383376743769257699376559-65976666
KC82162944392-540165411554157357393591354799-54093540415404254042357394306354016
KF302033--367713687036912368333699037514-36848368263682636826368333699837131
KF302034--129415128851129556129478128970129048-12949212947012874812947012947824884129441
KF302035351763517635176351793517635177386935176-35176351763517635175351773517635176
KF302036--377063782737869207983798138637-378053778337783377832079851038107
KF302037--445514465044692445584467826064-446284460644606446064455850744829
NC_0013306148-608961886230-6089650860346166613461346134-5156385
NC_00142254455158538653655355-5233535553735365536554314783--5365
NC_0217903854340089391913929038545228723916423054-38545385213852138521228723955239166
NC_0217947149971457714497154871590388807168669825-715267148571410714103888057272069
NC_0217967254172514725137263472676369451744972105-706427059870598705983694565672916
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC8216257664976666277387676576807-76666765503383376743769257699376559-54776666
KC82162944392-5401654115541578710511954799-5409354041540425404287104306354016
KF302033--367713687036912368333699037514-36848368263682636826368333699837131
KF302034--129415128851129556129478128970129048-129492129470128748129470129478690129441
KF302035351763517635176351793517635177259735176-35176351763517635175351773517635176
KF302036--37706378273786940563798138637-378053778337783377834056-38107
KF302037--445514465044692445584467819534-4462844606446064460644558-44829
NC_0013306148-608961886230-6089650860346166613461346134-5056385
NC_00142254455158538653655355-5233535553735365536554314783--5365
NC_0217903854340089391913929038545154863916417227-38545385213852138521154863955239166
NC_0217947149971457714497154871590128177168669825-715267148571410714101281750872069
NC_0217967254172514725137263472676258151283672105-7064270598705987059825815-72916
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC82162511111-1111111-461
KC8216291-111111-1111111
KF302033--11111111111111
KF302034--11111111111121
KF30203511111141-1111111
KF302036--111111111111331
KF302037--111111111111411
NC_0013301-111-1111111-61
NC_00142211111-1111111--1
NC_02179011111111-1111111
NC_02179411111111111111411
NC_02179611111121111111131
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC82162511211-1111111-771
KC8216291-111221-1111211
KF302033--11111111111111
KF302034--111111111111171
KF30203511111171-1111111
KF302036--111311111113-1
KF302037--111111111111-1
NC_0013301-111-1111111-91
NC_00142211111-1111111--1
NC_02179011111211-1111211
NC_02179411111311111113751
NC_02179611111231111112-1
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC82162511111-1121111-461
KC8216291-111111-1111111
KF302033--111111-1111111
KF302034--111111-1111121
KF30203511111141-1111111
KF302036--111111-11111331
KF302037--111111-11111411
NC_0013301-111-1111111-61
NC_00142211111-1111111--1
NC_02179011111111-1111111
NC_02179411111111-11111411
NC_02179611111121-11111131
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC82162511211-1121111-781
KC8216291-111221-1111211
KF302033--111111-1111111
KF302034--111111-11111171
KF30203511111171-1111111
KF302036--111311-11113-1
KF302037--111112-11111-1
NC_0013301-111-1111111-91
NC_00142211111-1111111--1
NC_02179011111212-1111211
NC_02179411111311-11113751
NC_02179611111231-11112-1
Misassemblies
1000000410000003
KC82162500000-0010000-00
KC8216291-00000000000000
KF302033--00000000000000
KF302034--00000100000002
KF3020350000000000000000
KF302036--00000000000000
KF302037--00000100000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000100000001
NC_0217940000000100000000
NC_0217960000000000000000
1000000410000003
   KC82162500000-0010000-00
   KC8216291-00000000000000
   KF302033--00000000000000
   KF302034--00000100000002
   KF3020350000000000000000
   KF302036--00000000000000
   KF302037--00000100000000
   NC_0013300-000-0000000-00
   NC_00142200000-0000000-00
   NC_0217900000000100000001
   NC_0217940000000100000000
   NC_0217960000000000000000
0000000000000000
   KC82162500000-0000000-00
   KC8216290-00000000000000
   KF302033--00000000000000
   KF302034--00000000000000
   KF3020350000000000000000
   KF302036--00000000000000
   KF302037--00000000000000
   NC_0013300-000-0000000-00
   NC_00142200000-0000000-00
   NC_0217900000000000000000
   NC_0217940000000000000000
   NC_0217960000000000000000
0000000000000000
   KC82162500000-0000000-00
   KC8216290-00000000000000
   KF302033--00000000000000
   KF302034--00000000000000
   KF3020350000000000000000
   KF302036--00000000000000
   KF302037--00000000000000
   NC_0013300-000-0000000-00
   NC_00142200000-0000000-00
   NC_0217900000000000000000
   NC_0217940000000000000000
   NC_0217960000000000000000
   # interspecies translocations0000000000000000
1000000410000002
KC82162500000-0010000-00
KC8216291-00000000000000
KF302033--00000000000000
KF302034--00000100000001
KF3020350000000000000000
KF302036--00000000000000
KF302037--00000100000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000100000001
NC_0217940000000100000000
NC_0217960000000000000000
5528700000029026276440000000209554
KC82162500000-00764400000-00
KC82162955287-00000000000000
KF302033--00000000000000
KF302034--000001313600000000153292
KF3020350000000000000000
KF302036--00000000000000
KF302037--000004559800000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_021790000000040281000000056262
NC_02179400000007302300000000
NC_0217960000000000000000
# possibly misassembled contigs0000000010000000
   # possible misassemblies0000000040000000
0139924423333226
KC82162500011-0010000-00
KC8216290-01100100000000
KF302033--11101101111011
KF302034--00100000000000
KF3020350000000010000000
KF302036--11111101111101
KF302037--11111001111101
NC_0013300-011-0100000-01
NC_00142200000-0000000-00
NC_0217900101000000000010
NC_0217940001101000000001
NC_0217960001100000000001
00500000160000000
KC82162500000-0000000-00
KC8216290-00000080000000
KF302033--00000010000000
KF302034--00000010000000
KF3020350050000020000000
KF302036--00000010000000
KF302037--00000010000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000000000000
NC_0217940000000010000000
NC_0217960000000010000000
Unaligned
# fully unaligned contigs5250114300000200151300496953
KC82162500000-0000000-00
KC8216290-00000000000000
KF302033--00000000000000
KF302034--00000000000000
KF3020350000000000000000
KF302036--00000000000000
KF302037--00000000000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000000000000
NC_0217940000000000000000
NC_0217960000000000000000
Fully unaligned length4523550453914453272860000014530056993960031252384491700
KC82162500000-0000000-00
KC8216290-00000000000000
KF302033--00000000000000
KF302034--00000000000000
KF3020350000000000000000
KF302036--00000000000000
KF302037--00000000000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000000000000
NC_0217940000000000000000
NC_0217960000000000000000
009700000140000000
KC82162500000-0010000-00
KC8216290-00000060000000
KF302033--00000010000000
KF302034--00000010000000
KF30203500970000010000000
KF302036--00000010000000
KF302037--00000010000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000000000000
NC_0217940000000010000000
NC_0217960000000010000000
0072903000003437040000000
KC82162500000-0063260000-00
KC8216290-000000141810000000
KF302033--000000256200000000
KF302034--000000953860000000
KF30203500729030000068640000000
KF302036--000000341170000000
KF302037--000000403850000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000000000000
NC_02179400000000615130000000
NC_02179600000000593120000000
Mismatches
271727272722929732727392821927
KC82162511111-113511131-11
KC8216290-00000110001000
KF302033--11111121111111
KF302034--00000050000010
KF3020350000001030000000
KF302036--00000000000010
KF302037--00000000000010
NC_0013309-999-9999999-79
NC_0014221616161616-16161616161616-616
NC_0217900000000010000000
NC_0217940000000000000010
NC_0217961000011110000100
22122218192521217823282724251627
KC82162500000-00441341-10
KC8216295-63475505766744
KF302033--22222201222222
KF302034--100200101101211
KF3020352222233222222322
KF302036--00000020000000
KF302037--00000030000000
NC_0013303-222-2253333-03
NC_00142211000-0040010-00
NC_0217902222252202222528
NC_0217947666645657766436
NC_0217962111122231111211
2673945181986215096240342244324986106102
KC82162500000-005537720427268-680
KC82162922-6347534081676666744
KF302033--22222201222222
KF302034--2400630078775505563242
KF3020352222233282222322
KF302036--000000460000000
KF302037--000000690000000
NC_00133061-222-225679474747-077
NC_0014225920000-004600450-00
NC_02179060222252202222528
NC_021794561466645681834266436
NC_02179671111222251111211
7.495.664.434.444.430.394.774.7758.364.434.436.414.60.393.844.43
KC8216251.31.31.311.31.3-1.31.3149.861.31.316.961.31-1.731.3
KC8216290-000001.8536.390001.85000
KF302033--2.722.722.722.722.722.7244.582.722.722.722.722.722.722.72
KF302034--00000031.04000000.850
KF3020350000002.840227.450000000
KF302036--0000000000004.770
KF302037--0000000000004.350
NC_001330147.86-147.86147.86147.86-147.86147.86147.88147.86147.86147.86147.86-159.31147.86
NC_001422297.07311.41297.07298.23298.79-305.75298.79298.79298.23298.23297.07298.23-338.79298.23
NC_0217900000000010000000000
NC_021794000000000000001.930
NC_0217961.3800001.381.381.3912.8500001.3800
6.143.612.963.124.843.453.4562.363.784.64.443.944.843.244.43
KC82162500000-0062.681.33.915.221.31-1.730
KC8216299.26-11.115.557.4113.059.269.2609.2612.9611.1111.1113.057.417.41
KF302033--5.445.445.445.435.445.4402.725.445.445.445.435.445.44
KF302034--0.77001.550062.080.770.7700.771.550.850.77
KF3020355.695.695.685.695.698.538.535.69151.635.695.695.695.698.535.695.69
KF302036--00000082.850000000
KF302037--000000100.70000000
NC_00133049.29-32.8632.8632.86-32.8632.8682.1649.2949.2949.2949.29-049.29
NC_00142218.5719.46000-0074.70018.570-00
NC_0217905.15.15.15.15.112.825.15.105.15.15.15.112.825.120.41
NC_0217949.88.48.48.48.45.6378.490.989.89.88.48.45.635.788.4
NC_0217962.761.381.381.381.382.762.762.7738.541.381.381.381.382.761.951.38
16102118192421202818201919241426
   KC82162500000-00140000-00
   KC8216294-63475404544744
   KF302033--22222201222222
   KF302034--00010070000101
   KF3020352222233212222322
   KF302036--00000000000000
   KF302037--00000000000000
   NC_0013302-222-2222222-02
   NC_00142200000-0010000-00
   NC_0217901222252202222528
   NC_0217946566645616666436
   NC_0217961111122221111211
62100101505885121
   KC82162500000-00301341-10
   KC8216291-00000101222000
   KF302033--00000000000000
   KF302034--10010031101110
   KF3020350000000010000000
   KF302036--00000020000000
   KF302037--00000030000000
   NC_0013301-000-0031111-01
   NC_00142211000-0030010-00
   NC_0217901000000000000000
   NC_0217941100000041100000
   NC_0217961000000010000000
379300000030966280023150001367
KC82162500000-1018240000-00
KC8216290-00000081650000003
KF302033--000000100760000001
KF302034--0000003548700000057
KF30203500000010436100000022
KF302036--00000030430000000
KF302037--00000047150000000
NC_0013300-000-00420000-00
NC_001422071000-001610000-00
NC_021790500000000310000000249
NC_02179400000000109260000000
NC_02179600000010168100000002
not_aligned3292290-----708--2315--01033
7.766.200000.460204470036.6900026.57
KC82162500000-1.1902386.190000-00
KC8216290-000000442480000005.54
KF302033--000000334680000002.69
KF302034--0000003190400000037.18
KF3020350000002.1204787000000062.45
KF302036--0000008340.410000000
KF302037--000000108900000000
NC_0013300-000-00696.060000-00
NC_00142201376.5000-002984.240000-00
NC_021790127.02000000056159000000442.57
NC_02179400000000163200000000
NC_0217960000001.250250620000002.74
not_aligned7.275.050-----48727--40.62--023
Statistics without reference
61561299121326891223141415271526538565
KC82162511211-4111111-981
KC8216291-111422181111421
KF302033--11111111111111
KF302034--111121111111741
KF3020351114411129131111111
KF302036--111511111115451
KF302037--111111111111491
NC_0013301-111-1111111-101
NC_00142211111-1111112-31
NC_0217902111236112222311
NC_02179411111421111114861
NC_021796111116191122226461
not_aligned52501143-----2--1513--496953
# contigs (>= 0 bp)3291563330121726198123715171045920263692871
55462421212234612171313333132312660
KC82162511211-4111111-101
KC8216291-11149171111421
KF302033--11111111111111
KF302034--111111111111101
KF302035112111114111111111
KF302036--11141111111401
KF302037--11111111111101
NC_0013301-111-1111111-01
NC_00142211111-1111111-01
NC_0217901111122101111211
NC_0217941111141111111471
NC_02179611111510112222561
not_aligned4740209-----0--320--8848
4337471212181512101212391118947
KC82162511211-1111111-01
KC8216291-11132101111321
KF302033--11111111111111
KF302034--11111111111131
KF3020351111111111111111
KF302036--11121111111201
KF302037--11111111111101
NC_0013301-111-1111111-01
NC_00142211111-1111110-01
NC_0217901111121101111211
NC_0217941111141111111401
NC_0217961111133111111311
not_aligned353134-----0--27--035
363342101013111071010331013840
KC82162511211-1111111-01
KC8216291-11111101111121
KF302033--11111111111111
KF302034--11111111111121
KF3020351111110101111111
KF302036--11111111111101
KF302037--11111111111101
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217901111121101111211
NC_0217941111131111111301
NC_0217961111123111111211
not_aligned302831-----0--23--030
322938101089107101029108534
KC82162511211-1111111-01
KC8216291-11111101111111
KF302033--11111111111111
KF302034--11111111111111
KF3020351111110101111111
KF302036--11101111111001
KF302037--11111111111101
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217901111101101111011
NC_0217941111111111111101
NC_0217961111121111111201
not_aligned262427-----0--19--024
242327551354552251029
KC82162511111-1111111-01
KC8216291-11100101111001
KF302033--00000000000000
KF302034--11111111111101
KF3020350000000000000000
KF302036--00000000000000
KF302037--00000000000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000000000001
NC_0217941111101111111001
NC_0217961111100111111001
not_aligned202022-----0--17--023
60603985009451784312951412955612947812965213136011123112949212947096143812947012947848827570751
KC8216257664976792528917676576807-76720766187644076743769257699376559-157977087
KC82162955287-540165411554157357693591354799497454093540415404254042357694316254124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--12941512951412955612947812965213136011123112949212947012947012947012947848827153292
KF302035351773517635384351813519335177702335176767935292352513517635214351773521435227
KF302036--37728378273786920798379813863736485378053778337783377832079885138107
KF302037--44551446504469244558446784559843295446284460644606446064455883944829
NC_0013306148-608961886230-6135650860346166613461346134-5626385
NC_00142254455158538653915377-5233537753955391539154314809-7645402
NC_021790385934008939191392903854522872391834028155238545385213852138521228723955256262
NC_0217947149971457714497154871590388817168673023669507152671485714107141038881244472069
NC_02179672541725147253572634726763694525697721056707570642705987059870598369452341972916
not_aligned606039850094517843-----759--961438--1713570751
488565948403306047398609973610384517099651026616996472579610018609790630914560935851709936599135144531
KC8216257664976792806297676576807-84099766187644076743769257699376559-6844377087
KC82162955287-5401654115541575384763083547991845354093540415404254042538475408154124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--129415129514129556129478130344131360111231129492129470129470129470129478127774153292
KF30203535177351761423523518135193351774727035176911035292352513517635214351773521435227
KF302036--3772837827378693429737981386373648537805377833778337783342972546938107
KF302037--4455144650446924455844678455984329544628446064460644606445582666944829
NC_0013306148-608961886230-6135650860346166613461346134-51926385
NC_00142254455158538653915377-5233537753955391539154315436-17825402
NC_021790393634008939191392903932539154428484028155239345392773927739277391543955256262
NC_02179471499714577144971548715907110072282730236695071526714857141071410711005925972069
NC_02179672541725147253572634726767265580083721056707572689726017260172601726555424272916
not_aligned452355045391445327286-----1453--5699396--31252384491700
Total length (>= 0 bp)4925478486478267935916099736112445170996836496169964760086101056099938733808609775517099150025775146971
48817644833798534492460997360960451482562293961699646839860921860903454986896079755148254124405140797
KC8216257664976792806297676576807-84099766187644076743769257699376559-1193877087
KC82162955287-5401654115541575384754245547991770854093540415404254042538475408154124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--12941512951412955612947812965213136011123112949212947012947012947012947891928153292
KF3020353517735176609993518135193351773700035176767935292352513517635214351773521435227
KF302036--377283782737869335463798138637364853780537783377833778333546038107
KF302037--445514465044692445584467845598432954462844606446064460644558044829
NC_0013306148-608961886230-6135650860346166613461346134-06385
NC_00142254455158538653915377-5233537753955391539154314809-05402
NC_0217903859340089391913929038545383844023440281038545385213852138521383843955256262
NC_02179471499714577144971548715907110071686730236695071526714857141071410711001243172069
NC_02179672541725147253572634726767190275006721056707572689726017260172601719023161572916
not_aligned452042545326124706165-----0--4889696--986834487966
48484524809805507217160997360960450028755229561699645069060717160703150783276011635002872691505110525
KC8216257664976792806297676576807-76720766187644076743769257699376559-077087
KC82162955287-540165411554157497994103254799054093540415404254042497995408154124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--12941512951412955612947812965213136011123112949212947012947012947012947879886153292
KF302035351773517635384351813519335177702335176767935292352513517635214351773521435227
KF302036--377283782737869271573798138637364853780537783377833778327157038107
KF302037--445514465044692445584467845598432954462844606446064460644558044829
NC_0013306148-608961886230-6135650860346166613461346134-06385
NC_00142254455158538653915377-5233537753955391539154310-05402
NC_0217903859340089391913929038545383843918340281038545385213852138521383843955256262
NC_0217947149971457714497154871590711007168673023669507152671485714107141071100072069
NC_02179672541725147253572634726766780155982721056707570642705987059870598678012341972916
not_aligned448711345086194459027-----0--4471337--04457694
47936024779566503860559839459799746914252878560511143158259561459550650389645950294691422629755062855
KC8216257664976792806297676576807-76720766187644076743769257699376559-077087
KC82162955287-540165411554157357693591354799054093540415404254042357695408154124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--12941512951412955612947812965213136011123112949212947012947012947012947873711153292
KF302035351773517635384351813519335177035176035292352513517635214351773521435227
KF302036--377283782737869207983798138637364853780537783377833778320798038107
KF302037--445514465044692445584467845598432954462844606446064460644558044829
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217903859340089391913929038545383843918340281038545385213852138521383843955256262
NC_0217947149971457714497154871590653857168673023669507152671485714107141065385072069
NC_02179672541725147253572634726766276055982721056707570642705987059870598627602341972916
not_aligned444385644835384436936-----0--4443539--04421811
47279434712281497582859839459799738345649850060511143158259561459550649765565950293834562037534961380
KC8216257664976792806297676576807-76720766187644076743769257699376559-077087
KC82162955287-540165411554157357693591354799054093540415404254042357694316254124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--12941512951412955612947812965213136011123112949212947012947012947012947848827153292
KF302035351773517635384351813519335177035176035292352513517635214351773521435227
KF302036--3772837827378690379813863736485378053778337783377830038107
KF302037--445514465044692445584467845598432954462844606446064460644558044829
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_02179038593400893919139290385450391834028103854538521385213852103955256262
NC_0217947149971457714497154871590388817168673023669507152671485714107141038881072069
NC_0217967254172514725357263472676627602569772105670757064270598705987059862760072916
not_aligned437819744162534374159-----0--4381131--04320336
440163444479614535797404576404786129478278058407905321696402496402519468615740207912947804759938
KC8216257664976792528917676576807-76720766187644076743769257699376559-077087
KC82162955287-54016541155415700547990540935404154042540420054124
KF302033--00000000000000
KF302034--1294151295141295561294781296521313601112311294921294701294701294701294780153292
KF3020350000000000000000
KF302036--00000000000000
KF302037--00000000000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_02179000000000000000056262
NC_02179471499714577144971548715900716867302366950715267148571410714100072069
NC_0217967254172514725357263472676007210567075706427059870598705980072916
not_aligned412565842271984155491-----0--4283644--04274188
23257224699814764471548715903683339183721056707570642705982344137059836833633197323
KC8216257664976792528917676576807-76720766187644076743769257699376559-67677087
KC82162955287-540165411554157357693591354799243754093540415404254042357694316254124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--12941512951412955612947812965213136011123112949212947012947012947012947824884153292
KF3020353517735176896351813519335177277035176767935292352513517635214351773521435227
KF302036--37728378273786920798379813863736485378053778337783377832079853538107
KF302037--44551446504469244558446784559843295446284460644606446064455852144829
NC_0013306148-608961886230-6135650860346166613461346134-5166385
NC_00142254455158538653915377-5233537753955391539154314809-5125402
NC_021790385934008939191392903854522872391834028155238545385213852138521228723955256262
NC_021794714997145771449715487159038881716867302366950715267148571410714103888161772069
NC_0217967254172514725357263472676369451744972105670757064270598705987059836945187572916
not_aligned242354246998183441-----759--254168--622270337
108259113859528913929038545228722569740281432953854538521490813852122872551107191
KC8216257664976792277387676576807-76720766187644076743769257699376559-58677087
KC82162955287-540165411554157871023225479915875409354041540425404287104316254124
KF302033--3677136870369123683336990375143010636848368263682636826368333699837131
KF302034--129415129514129556129478129652131360111231129492129470129470129470129478694153292
KF3020353517735176638351813519335177104535176767935292352513517635214351773521435227
KF302036--377283782737869635937981386373648537805377833778337783635951038107
KF302037--44551446504469244558446784559843295446284460644606446064455851044829
NC_0013306148-608961886230-6135650860346166613461346134-5066385
NC_00142254455158538653915377-5233537753955391539154314809-5065402
NC_021790385934008939191392903854515512391834028155238545385213852138521155123955256262
NC_021794714997145771449715487159012817716867302366950715267148571410714101281752372069
NC_02179672541725147253572634726762581546427210567075706427059870598705982581554972916
not_aligned12803814785356152-----694--53841--549120025
86114455434484520788
KC82162511111-1111111-401
KC8216291-11111131111111
KF302033--11111111111111
KF302034--11111111111121
KF30203511321116111111111
KF302036--111111111111211
KF302037--111111111111231
NC_0013301-111-1111111-51
NC_00142211111-1111111-21
NC_0217901111111111111111
NC_02179411111111111111311
NC_0217961111112111111131
not_aligned769-----1--7--21306
161327779975772379362617
KC82162511211-1111111-671
KC8216291-11125151111211
KF302033--11111111111111
KF302034--111111111111161
KF302035118111113111111111
KF302036--111211111112331
KF302037--111111111111361
NC_0013301-111-1111111-81
NC_00142211111-1111111-31
NC_0217901111121111111211
NC_02179411111311111113571
NC_02179611111241111112201
not_aligned131120-----2--17--346613
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
KC82162530.2230.2330.1830.2230.22-30.1330.2230.2230.2230.2330.2630.22-29.9230.25
KC82162933.43-33.4733.4633.4833.4533.2333.4533.2733.4633.4733.4733.4733.4533.4833.48
KF302033--40.5140.5240.5140.5240.5140.540.4240.540.5140.4840.5140.5240.5140.52
KF302034--35.7335.7335.7335.7335.7135.6535.7535.7335.7435.7435.7335.7335.7735.44
KF30203544.9144.9140.4344.9144.944.9144.6244.9146.3944.8844.9144.9144.9144.9144.8844.88
KF302036--40.2140.2240.2140.1640.2240.1540.1940.2140.2140.240.2140.1639.8140.22
KF302037--44.6544.6744.6844.6644.6944.6444.6444.6744.6644.6644.6744.6644.4144.72
NC_00133045.22-45.2145.4145.35-45.1244.9945.1845.3145.1945.1945.19-47.0344.96
NC_00142244.744.6444.6944.744.71-44.8944.7144.7544.744.744.6744.68-46.0744.67
NC_02179036.536.4336.5136.536.536.5536.4836.6536.7836.536.536.536.536.5536.5235.87
NC_02179432.8832.8832.8832.8832.8932.8832.9632.832.8132.8932.8832.8832.8832.8832.5432.91
NC_02179638.0538.0538.0538.0538.0638.0437.8938.0637.8538.0638.0638.0638.0538.0437.8238.06
not_aligned34.6334.6535.37-----34.9--35.62--34.2934.6
Predicted genes
Similarity statistics
2211111202222112
KC82162511000-1101111-01
KC8216290-00000000000000
KF302033--00000000000000
KF302034--00000000000000
KF3020351111110101111111
KF302036--00000000000000
KF302037--00000000000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000000000000
NC_0217940000000000000000
NC_0217960000000000000000
0000000000000000
KC82162500000-0000000-00
KC8216290-00000000000000
KF302033--00000000000000
KF302034--00000000000000
KF3020350000000000000000
KF302036--00000000000000
KF302037--00000000000000
NC_0013300-000-0000000-00
NC_00142200000-0000000-00
NC_0217900000000000000000
NC_0217940000000000000000
NC_0217960000000000000000
Plots:ContigsLargest alignmentTotal aligned lenMisassembliesMis. lenMismatchesIndelsN's per 100 kbpGenome frac.Dup. ratioNGA50
0
20
40
60
80
100
120
140
Contigs = 160
Sort references by:

ReferenceSize, bpFragmentsGC, %
KC82162576666130.22
KC82162954012133.48
KF30203337211140.53
KF302034129439135.73
KF30203535330144.87
KF30203638208140.23
KF30203745035144.67
NC_0013306087145.18
NC_0014225386144.76
NC_02179039189136.52
NC_02179471443132.88
NC_02179672534138.06
610540


Not aligned contigs

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{}
{}
{"links_names":["View in Icarus contig browser"],"links":["icarus.html"]}
{ "# contigs" : "is the total number of contigs in the assembly.", "Largest contig" : "is the length of the longest contig in the assembly.", "Total length" : "is the total number of bases in the assembly.", "Reference length" : "is the total number of bases in the reference.", "# contigs (>= 0 bp)" : "is the total number of contigs in the assembly that have size greater than or equal to 0 bp.", "Total length (>= 0 bp)" : "is the total number of bases in the contigs having size greater than or equal to 0 bp.", "N50" : "is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly. Usually there is no value that produces exactly 50%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 50% of the total assembly length.", "NG50" : "is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "N75" : "is the contig length such that using longer or equal length contigs produces 75% of the bases of the assembly. Usually there is no value that produces exactly 75%, so the technical definition is the maximum length x such that using contigs of length at least x accounts for at least 75% of the total assembly length.", "NG75" : "is the contig length such that using longer or equal length contigs produces 75% of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "L50" : "is the minimum number of contigs that produce half (50%) of the bases of the assembly. In other words, it's the number of contigs of length at least N50.", "LG50" : "is the minimum number of contigs that produce half (50%) of the bases of the reference genome. In other words, it's the number of contigs of length at least NG50. This metric is computed only if a reference genome is provided.", "L75" : "is the minimum number of contigs that produce 75% of the bases of the assembly. In other words, it's the number of contigs of length at least N75.", "LG75" : "is the minimum number of contigs that produce 75% of the bases of the reference genome. In other words, it's the number of contigs of length at least NG75. This metric is computed only if a reference genome is provided.", "NA50" : "is N50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NGA50" : "is NG50 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NA75" : "is N75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "NGA75" : "is NG75 where the lengths of aligned blocks are counted instead of contig lengths. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces. This metric is computed only if a reference genome is provided.", "LA50" : "is L50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LGA50" : "is LG50 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LA75" : "is L75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "LGA75" : "is LG75 where aligned blocks are counted instead of contigs. I.e., if a contig has a misassembly with respect to the reference, the contig is broken into smaller pieces.", "Average %IDY" : "is the average of alignment identity percent (Nucmer measure of alignment accuracy) among all contigs.", "# misassemblies" : "is the number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).", "# misassembled contigs" : "is the number of contigs that contain misassembly events.", "Misassembled contigs length" : "is the number of total bases contained in all contigs that have one or more misassemblies.", "# relocations" : "is the number of relocation events among all misassembly events. Relocation is a misassembly where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference, or they overlap by more than 1 kbp and both flanking sequences align on the same chromosome.", "# translocations" : "is the number of translocation events among all misassembly events. Translocation is a misassembly where the flanking sequences align on different chromosomes.", "# interspecies translocations" : "is the number of interspecies translocation events among all misassembly events. Interspecies translocation is a misassembly where the flanking sequences align on different references (--meta only).", "# inversions" : "is the number of inversion events among all misassembly events. Inversion is a misassembly where it is not a relocation and the flanking sequences align on opposite strands of the same chromosome.", "# local misassemblies" : "is the number of local misassemblies. We define a local misassembly breakpoint as a breakpoint that satisfies these conditions:
  1. Two or more distinct alignments cover the breakpoint.
  2. The gap between left and right flanking sequences is less than 1 kbp.
  3. The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.
", "# scaffold gap size misassemblies" : "is the number of scaffold gap size misassemblies. We define scaffold gap size misassembly as a breakpoint where the flanking sequences combined in scaffold on the wrong distance. These misassemblies are not included in the total number of misassemblies. ", "# possibly misassembled contigs": "is the number of contigs that contain large unaligned fragment (default min length is 500 bp) and thus could possibly contain interspecies translocation with unknown reference.", "# possible misassemblies" : "is the number of putative interspecies translocations in possibly misassembled contigs if each large unaligned fragment is supposed to be a fragment of unknown reference.", "# structural variations" : "is the number of misassemblies matched with structural variations.", "# unaligned mis. contigs" : "is the number of contigs that have the number of unaligned bases more than 50% of contig length and a misassembly event in their aligned fragment. Note that such misassemblies are not counted in # misassemblies and other misassemblies statistics.", "# fully unaligned contigs" : "is the number of contigs that have no alignment to the reference sequence.", "Fully unaligned length" : "is the total number of bases contained in all fully unaligned contigs.", "# partially unaligned contigs" : "is the number of contigs that have at least one alignment to the reference sequence but also have at least one unaligned fragment of length ≥ unaligned-part-size threshold.", "Partially unaligned length" : "is the total number of unaligned bases in all partially unaligned contigs.", "# ambiguous contigs" : "is the number of contigs that have reference alignments of equal quality in multiple locations on the reference.", "Ambiguous contigs length" : "is the total number of bases contained in all ambiguous contigs.", "Genome fraction (%)" : "is the total number of aligned bases in the reference, divided by the genome size. A base in the reference genome is counted as aligned if there is at least one contig with at least one alignment to this base. Contigs from repeat regions may map to multiple places, and thus may be counted multiple times in this quantity.", "GC (%)" : "is the total number of G and C nucleotides in the assembly, divided by the total length of the assembly.", "Reference GC (%)" : "is the total number of G and C nucleotides in the reference, divided by the total length of the reference.", "# mismatches per 100 kbp" : "is the average number of mismatches per 100000 aligned bases.", "# mismatches" : "is the number of mismatches in all aligned bases.", "# indels per 100 kbp" : "is the average number of indels per 100000 aligned bases.", "# indels" : "is the number of indels in all aligned bases", "# indels (<= 5 bp)" : "is the number of indels of length less than or equal to 5 bp", "# indels (> 5 bp)" : "is the number of indels of length greater than 5 bp", "Indels length" : "is the number of total bases contained in all indels", "# genes" : "is the number of genes in the assembly (complete and partial), based on a user-provided annotated list of gene positions in the reference genome. A gene counts as 'partially covered' if the assembly contains at least 100 bp of this gene but not the whole gene.", "# operons" : "is the number of operons in the assembly (complete and partial), based on a user-provided annotated list of operon positions in the reference genome. An operon counts as 'partially covered' if the assembly contains at least 100 bp of this operon but not the whole operon.", "# predicted genes (unique)" : "is the number of unique genes in the assembly found by a gene prediction tool.", "# predicted genes (>= 0 bp)" : "is the number of found genes having length greater than or equal to 0 bp.", "Cumulative length" : "plot shows the growth of assembly contig lengths. On the x-axis, contigs are ordered from largest (contig #1) to smallest. The y-axis gives the size of the x largest contigs in the assembly.", "Nx" : "plot shows the Nx metric value as x varies from 0 to 100. Nx is the minimum contig length y such that using contigs of length at least y accounts for at least x% of the total assembly length.", "NGx" : "plot shows the NGx metric value as x varies from 0 to 100. NGx is the minimum contig length y such that using contigs of length at least y accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "NAx" : "plot shows the NAx metric value as x varies from 0 to 100. NAx is computed similarly to Nx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken into aligned blocks at misassembly breakpoints. NAx is the minimum block length y such that using blocks of length at least y accounts for at least x% of the bases of the assembly. This metric is computed only if a reference genome is provided.", "NGAx" : "plot shows the NGAx metric value as x varies from 0 to 100.NGAx is computed similarly to NGx, but based on lengths of aligned blocks instead of contig lengths. Contigs are broken at misassembly breakpoints. NGAx is the minimum block length y such that using blocks of length at least y accounts for at least x% of the bases of the reference genome. This metric is computed only if a reference genome is provided.", "GC content" : "plot shows the distribution of GC percentage among the contigs, i.e., the total number of bases in contigs with such GC content. Typically, the distribution is approximately Gaussian. However, for some genomes it is not Gaussian. For assembly projects with contaminants, the GC distribution of the contaminants often differs from the reference genome and may give a superposition of multiple curves with different peaks.", "Duplication ratio" : "is the total number of aligned bases in the assembly (i.e. Total length - Fully unaligned length - Partially unaligned length), divided by the total number of aligned bases in the reference (see the Genome fraction (%) metric). If the assembly contains many contigs that cover the same regions of the reference, its Duplication ratio may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.", "Largest alignment" : "is the length of the largest continuous alignment in the assembly. This metric is always equal to the Largest contig metric but it can be smaller if the largest contig of the assembly contains a misassembly event.", "Total aligned length" : "is the total number of aligned bases in the assembly.", "Avg contig read support" : "is the average coverage of contigs that have large unique alignments to the reference. Read coverage is extracted from contig names (SPAdes/Velvet naming scheme only).", "# N's" : "is the total number of uncalled bases (N's) in the assembly.", "# N's per 100 kbp" : "is the average number of uncalled bases (N's) per 100000 assembly bases.", "# similar correct contigs" : "is the number of correct contigs similar among > 50% assemblies (see Icarus for visualization).", "# similar misassembled blocks" : "is the number of misassembled blocks similar among > 50% assemblies (see Icarus for visualization)." }