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":"28 December 2014, Sunday, 19:38:55","report":[["Statistics without reference",[{"values":[4,52,44,76,6,6,3],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[4,52,44,76,6,6,3],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[4,52,44,76,6,6,3],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[3161528,300351,500181,250537,2045299,2044231,3622857],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4662182,4441307,4483671,4298734,4637078,4631147,4635596],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4662182,4441307,4483671,4298734,4637078,4631147,4635596],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4662182,4441307,4483671,4298734,4637078,4631147,4635596],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[3161528,93960,113089,63438,1293638,1522515,3622857],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[707167,77697,84049,41498,805919,1522515,3622857],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,14,12,19,2,2,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[2,27,23,40,3,2,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.80","50.95","50.89","50.96","50.81","50.82","50.81"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[8,6,7,7,7,7,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[7,6,7,7,7,7,7],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[1,0,0,0,0,0,1],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1,3,4,4,3,2,1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[3161528,678927,950772,526030,3567978,3566746,3622857],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[2,2,4,2,2,2,2],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[15,69,73,144,17,9,16],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[198,2477,1773,2867,490,448,506],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[224,2832,2028,3395,579,482,617],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.32","1.56","1.63","3.36","0.37","0.19","0.35"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["4.27","55.84","39.54","66.83","10.58","9.68","10.92"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[196,2456,1759,2836,487,445,499],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[2,21,14,31,3,3,7],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.00","0.00","0.00","0.00","0.00","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.938","95.614","96.642","92.463","99.831","99.757","99.862"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.005","1.001","1.000","1.002","1.001","1.001","1.001"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4490 + 5 part","4230 + 70 part","4293 + 65 part","4105 + 105 part","4481 + 10 part","4474 + 12 part","4487 + 6 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[949260,248433,330053,250537,1096469,1095712,1096619],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[3161528,91701,113089,57390,1293638,1522515,3622857],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[707167,71257,79480,38411,805919,1522515,3622857],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[702757,91616,111935,57390,857595,857662,910332],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[572321,71257,73785,40860,805919,771141,804398],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[702757,89630,111935,53224,857595,857662,910332],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[572321,64275,70260,36774,805919,771141,804398],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,15,12,22,2,2,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[2,29,25,47,3,2,1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[3,15,13,21,3,3,3],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[5,28,25,43,4,4,4],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[3,16,13,24,3,3,3],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[5,31,27,50,4,4,4],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675,4639675,4639675,4639675,4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79","50.79","50.79","50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497,4497,4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4,5,6],"assembliesNames":["f25_d6_all","f25_d6_rg4_1","f25_d6_rg4_2","f25_d6_rg4_3","f25_d6_rg6_1","f25_d6_rg6_2","f25_d6_rg6_3"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"f25_d6_all":[3064,682,386,358],"f25_d6_rg6_3":[3507,777,203],"f25_d6_rg6_2":[1957,1485,742,201,56,33],"f25_d6_rg6_1":[1958,1246,780,239,200,58],"f25_d6_rg4_1":[316,239,221,161,164,152,145,115,122,118,108,121,97,88,79,90,91,84,75,76,78,86,70,76,72,76,78,66,75,66,87,59,53,52,61,49,49,40,36,29,32,33,39,33,28,31,23,25,15,19,21,11],"f25_d6_rg4_3":[249,173,181,111,127,124,137,112,126,103,96,82,77,74,73,94,60,63,61,49,63,52,49,57,56,42,49,40,53,48,37,43,40,44,43,42,39,45,37,39,37,38,35,36,35,32,36,38,32,33,40,33,34,38,38,27,30,34,32,34,30,27,25,24,21,27,24,24,22,11,18,16,11,16,13,14],"f25_d6_rg4_2":[506,229,225,223,178,142,152,138,132,118,138,109,104,105,91,81,92,96,93,83,85,78,68,77,80,63,64,60,63,61,56,61,52,48,49,51,38,33,37,38,28,31,20,17]},"filenames":["f25_d6_all","f25_d6_rg4_1","f25_d6_rg4_2","f25_d6_rg4_3","f25_d6_rg6_1","f25_d6_rg6_2","f25_d6_rg6_3"]}
{{ 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 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.",
"# 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.