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":"25 July 2014, Friday, 16:57:50","report":[["Statistics without reference",[{"values":[26,23,18,17,14],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[26,23,18,17,14],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[26,23,18,17,14],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[500519,1040738,671836,803212,1099298],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4663672,4668811,4688223,4693002,4703352],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4663672,4668811,4688223,4693002,4703352],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4663672,4668811,4688223,4693002,4703352],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[245130,484760,462620,508833,544950],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[165612,136338,268654,307063,362655],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[7,3,5,4,4],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[13,8,8,7,6],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.78","50.79","50.79","50.83","50.79"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[8,10,13,9,11],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[7,10,12,9,10],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[1,0,1,0,1],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[3,6,4,5,6],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[708152,2407429,1389781,1480741,2433888],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[5,3,6,5,9],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[406,393,416,438,325],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[119,76,94,45,31],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[207,94,147,65,36],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["8.76","8.50","8.99","9.48","7.01"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["2.57","1.64","2.03","0.97","0.67"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[117,76,92,44,31],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[2,0,2,1,0],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[4,2,1,1,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.09","0.04","0.02","0.02","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.895","99.596","99.746","99.548","99.931"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.006","1.011","1.014","1.016","1.014"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4478 + 16 part","4474 + 12 part","4477 + 9 part","4470 + 8 part","4489 + 6 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[500519,798543,599418,803212,613627],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[245130,484760,462620,508833,544950],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[165612,136338,268654,307063,362655],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[187140,407626,275303,477000,526088],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[137262,136317,144328,305007,360851],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[187140,407626,275303,477000,526088],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[137262,136317,194324,305007,360851],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[7,3,5,4,4],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[13,8,8,7,6],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[8,4,6,4,5],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[15,10,11,7,7],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[8,4,6,4,5],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[15,10,10,7,7],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675,4639675,4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79","50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4],"assembliesNames":["192221_asm.ctg","210845_asm.ctg","2_asm.ctg","3_asm.ctg","4_asm.ctg"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"192221_asm.ctg":[482,360,332,376,278,314,228,181,163,175,170,154,166,155,145,137,112,122,107,87,51,60,42,42,20,19],"210845_asm.ctg":[1025,970,469,374,200,159,137,135,99,109,122,83,98,95,86,82,51,52,40,38,22,15,13],"4_asm.ctg":[1074,595,572,510,475,352,247,162,96,98,98,77,74,59],"3_asm.ctg":[770,718,586,479,397,293,290,229,176,160,113,90,92,38,12,19,8],"2_asm.ctg":[678,557,457,436,449,359,326,265,192,144,137,122,93,85,54,55,36,32]},"filenames":["192221_asm.ctg","210845_asm.ctg","2_asm.ctg","3_asm.ctg","4_asm.ctg"]}
{{ 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.