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":"15 August 2014, Friday, 15:33:43","report":[["Statistics without reference",[{"values":[16,28,23],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[57,1025,1012],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[15,15,10],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[1090659,1749262,3014973],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4611695,4630525,4634373],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4617459,4879656,4881813],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4611011,4622377,4626225],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[692096,1092719,3014973],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[499932,694449,692286],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[3,2,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[5,3,2],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.77","50.73","50.74"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[5,3,1],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[5,3,1],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[3,2,1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[1844546,2841981,3014973],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[20,7,6],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,16,16],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,13667,13667],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[431,398,402],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[35,39,29],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[50,55,53],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["9.36","8.62","8.70"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.76","0.85","0.63"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[35,39,27],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[0,0,2],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[4264,1450,368],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["92.46","31.31","7.94"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.217","99.459","99.605"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.002","1.001","1.001"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4459 + 13 part","4470 + 13 part","4479 + 3 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[1090429,1093845,2497974],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[692096,1092719,3014973],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[499932,694449,692286],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[657193,694449,2497974],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[333404,500381,654225],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[657193,694449,2497974],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[333404,500381,654225],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[3,2,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[5,3,2],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[3,3,1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[6,5,3],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[3,3,1],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[6,5,3],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2],"assembliesNames":["spd_d1_web","spd_d1_raw","spd_d1_raw_d5_single"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[1090659,785587,692096,559027,499932,499897,177876,138934,88914,36418,33934,2936,2463,1334,1004,684],[1749262,1092719,694449,500381,175864,139915,128203,92566,38338,2569,2079,1971,1857,1111,1093,928,865,782,640,637,631,543,535,533,521,518,511,504],[3014973,692286,654225,167471,88669,2569,1971,1857,1111,1093,928,865,782,640,637,631,543,535,533,521,518,511,504]],"filenames":["spd_d1_web","spd_d1_raw","spd_d1_raw_d5_single"]}
{"lists_of_lengths":[[1090429,692096,657193,499776,359490,333404,192852,177876,166528,138934,127885,88750,36418,33934,3252,2936,2463,1334,1004,684,113],[1093845,700096,694449,655014,500381,199957,191619,175864,139915,128203,92566,38338,2079,1971,1111],[2497974,692286,654225,516648,167471,88669,1971,1111]],"filenames":["spd_d1_web","spd_d1_raw","spd_d1_raw_d5_single"]}
{"assemblies_lengths":[4611695,4630525,4634373],"filenames":["spd_d1_web","spd_d1_raw","spd_d1_raw_d5_single"]}
{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"spd_d1_raw_d5_single":[2953,677,608,153,88,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"spd_d1_web":[1069,724,677,531,505,507,171,119,89,36,29,0,0,1,1,0],"spd_d1_raw":[1680,1065,679,508,171,121,116,90,38,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]},"filenames":["spd_d1_web","spd_d1_raw","spd_d1_raw_d5_single"]}
{{ 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.