QUAST report
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Contigs are ordered from largest (contig #1) to smallest. Contigs are broken into nonoverlapping 100 bp windows. Plot shows numbers of windows for each GC percentage. |
{"date":"29 July 2013, Monday, 09:57:57","report":[["Basic statistics",[{"values":[382,131,52,733,185,40,143,35],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[382,131,52,733,185,40,143,35],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[339,131,47,656,180,32,130,35],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[71578,177098,241348,44874,204500,739647,236829,740054],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4503182,3953489,4247061,4091078,4549335,4781613,4526809,4950301],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4503182,3953489,4247061,4091078,4549335,4781613,4526809,4950301],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4474301,3953489,4243514,4032589,4545945,4776482,4518112,4950301],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[4603060,4603060,4603060,4603060,4603060,4603060,4603060,4603060],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":[22050,45887,165131,9086,45133,518052,88399,492976],"quality":"More is better","isMain":false,"metricName":"N50"},{"values":[11736,25501,104435,4930,27903,204947,39660,205410],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[21441,40287,144812,7971,45133,518052,85272,523557],"quality":"More is better","isMain":true,"metricName":"NG50"},{"values":[11021,16846,77487,3567,26996,235182,37869,236526],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[67,26,11,136,32,4,17,5],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[137,55,19,291,63,8,36,8],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":[70,33,12,166,32,4,18,4],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[144,79,22,381,65,7,37,7],"quality":"Less is better","isMain":false,"metricName":"LG75"}]],["Misassemblies",[{"values":[2,6,5,0,3,9,17,24],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[1,3,3,0,1,5,11,13],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[1,3,2,0,2,4,6,11],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1,5,4,0,3,7,11,16],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[24651,135726,40523,0,24631,1180537,564277,1850338],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[3,7,8,2,219,8,190,15],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0,0,1,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,0,566,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[3,1,1,1,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[152,78,23,96,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Genome statistics",[{"values":["97.529","85.608","91.915","87.770","98.068","99.370","97.437","99.474"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.003","1.024","1.009","1.007","1.017","1.045","1.008","1.082"],"quality":"Less is better","isMain":false,"metricName":"Duplication ratio"},{"values":["4030 + 275 part","3685 + 128 part","4036 + 38 part","3348 + 592 part","4046 + 307 part","4347 + 23 part","4068 + 265 part","4358 + 19 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":["68.77","69.06","68.90","69.03","68.83","68.88","68.77","68.82"],"quality":"Equal","isMain":false,"metricName":"GC (%)"},{"values":["68.79","68.79","68.79","68.79","68.79","68.79","68.79","68.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":["4.83","10.51","12.48","3.22","5.98","5.82","13.11","6.42"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":[217,414,528,130,270,266,588,294],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":["3.43","7.97","5.84","3.34","3.90","3.63","8.34","3.69"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[154,314,247,135,176,166,374,169],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[149,304,238,133,169,157,359,160],"quality":"Less is better","isMain":false,"metricName":" # short indels (<= 5 bp)"},{"values":[5,10,9,2,7,9,15,9],"quality":"Less is better","isMain":false,"metricName":" # long indels (> 5 bp)"},{"values":[233,447,400,187,254,351,650,355],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":[0,821,205,0,6334,0,33457,182],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","20.77","4.83","0.00","139.23","0.00","739.09","3.68"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Aligned statistics",[{"values":[71578,177098,241348,44874,204215,739647,234789,740054],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[22050,42489,165131,9086,45022,518052,84960,492884],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[11706,24136,104435,4922,27902,200493,37869,200586],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[21441,36097,144812,7971,45022,518052,84960,518314],"quality":"More is better","isMain":false,"metricName":"NGA50"},{"values":[11021,16846,77487,3560,26839,200509,33962,200602],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[67,27,11,136,32,4,18,5],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[138,58,19,291,63,9,37,9],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[70,35,12,166,32,4,18,4],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[144,81,22,382,65,8,39,8],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]]],"minContig":500,"assembliesNames":["abyss_scf","cabog_scf","msrca_scf","sga_scf","soap_scf","spades2.5_scf","velvet_scf","CISA_result"]}
{{ qualities }}
{{ mainMetrics }}
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{"assemblies_lengths":[4503182,3953489,4247061,4091078,4549335,4781613,4526809,4950301],"filenames":["abyss_scf","cabog_scf","msrca_scf","sga_scf","soap_scf","spades2.5_scf","velvet_scf","CISA_result"]}
{"reflen":4603060}
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{{ operonsInContigs }}
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{
"# 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.",
"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 minimum 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 minimum 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.",
" # 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:
- Two or more distinct alignments cover the breakpoint.
- The gap between left and right flanking sequences is less than 1 kbp.
- The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.