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, 19:14:25","report":[["Statistics without reference",[{"values":[2,51,45,74,10,7,7],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[2,51,45,74,10,7,7],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[2,51,45,74,10,7,7],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[3835918,300357,499793,250543,1068976,2044231,2177132],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4640911,4429199,4462499,4252687,4637980,4633643,4641751],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4640911,4429199,4462499,4252687,4637980,4633643,4641751],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4640911,4429199,4462499,4252687,4637980,4633643,4641751],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[3835918,108839,113115,69767,674174,1522440,1026958],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[3835918,77698,82500,41499,376247,1522440,770508],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,13,12,19,3,2,2],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,26,23,40,5,2,3],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.79","50.96","50.88","50.95","50.83","50.82","50.82"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[8,6,7,5,8,8,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[7,6,7,5,8,8,7],"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":[1,3,4,3,4,3,2],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[3835918,677539,950434,397273,3005363,3623486,3204090],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[2,2,4,2,2,2,3],"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":[11,74,70,140,36,14,14],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[277,2439,1760,2798,554,525,476],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[318,2778,1963,3206,673,595,605],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.24","1.67","1.57","3.30","0.78","0.30","0.30"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["5.97","55.08","39.44","66.00","11.98","11.35","10.28"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[274,2419,1750,2771,550,520,472],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[3,20,10,27,4,5,4],"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","95.440","96.187","91.369","99.687","99.723","99.832"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.001","1.000","1.000","1.004","1.004","1.002","1.002"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4490 + 5 part","4221 + 75 part","4274 + 65 part","4056 + 105 part","4467 + 13 part","4471 + 13 part","4484 + 9 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[1123148,248438,330045,250543,1067435,1095707,949218],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[3835918,105835,113115,58883,674174,1522440,1026958],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[3835918,71257,71590,38394,376247,1522440,770508],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[949257,93295,111934,58883,618553,857595,770508],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[804993,71257,71590,40797,315961,497280,402998],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[949257,91700,98451,53254,618553,857595,770508],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[804993,62388,67255,36776,315961,497280,402998],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,14,12,22,3,2,2],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,28,25,47,5,2,3],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[3,14,13,21,3,3,3],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[4,27,25,43,6,5,5],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[3,15,14,24,3,3,3],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[4,30,27,50,6,5,5],"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":[3714,776],"f25_d6_rg6_3":[2111,994,741,343,202,58,35],"f25_d6_rg6_2":[1957,1485,482,256,201,57,33],"f25_d6_rg6_1":[1004,1020,679,566,358,302,236,142,108,52],"f25_d6_rg4_1":[316,238,221,185,161,164,152,145,115,121,108,121,105,97,87,79,91,76,74,78,86,70,76,72,76,78,66,75,87,59,53,52,61,49,49,49,40,29,32,35,33,31,39,33,28,31,23,25,19,21,10],"f25_d6_rg4_3":[249,173,135,124,128,137,112,119,103,96,106,82,77,74,73,94,66,76,59,61,56,49,63,51,57,42,49,40,53,48,37,43,40,44,43,42,39,45,37,39,38,35,37,36,35,32,36,38,32,40,33,33,38,38,27,30,34,32,34,30,25,27,25,36,24,23,27,24,24,11,18,16,11,16],"f25_d6_rg4_2":[506,229,225,223,178,152,138,129,132,118,138,109,104,105,91,81,92,96,93,83,85,68,77,80,63,64,60,59,63,61,56,61,52,48,49,51,38,33,37,38,28,31,17,18,15]},"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.