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, 16:21:43","report":[["Statistics without reference",[{"values":[86,15,18,16,15,17,14],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[546,462,457,451,452,451,450],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[73,11,13,10,10,12,7],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[285889,2497845,1260980,2501081,3194637,1954649,3392211],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4577132,4632909,4633058,4636174,4638657,4633857,4632677],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4696376,4748143,4746108,4748681,4751462,4746289,4746083],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4567893,4630404,4629941,4632414,4635540,4630553,4628111],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[139882,2497845,1238868,2501081,3194637,1238635,3392211],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[78649,327068,425744,302458,326982,366279,367606],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[11,1,2,1,1,2,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[22,3,4,3,2,3,2],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.74","50.77","50.77","50.76","50.77","50.76","50.77"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[2,9,10,10,10,8,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[2,9,10,10,10,8,8],"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":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[2,2,6,3,4,4,3],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[215581,3193893,3244631,2705788,3657574,3243566,4020696],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[4,15,18,12,13,14,21],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[5,5,5,6,5,6,6],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[7968,7968,7968,8611,7968,9778,8641],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0,0,1],"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":[0,0,0,0,0,0,346],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[138,330,286,319,332,279,297],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[21,49,46,61,59,44,49],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[29,96,147,382,324,92,246],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["3.02","7.15","6.20","6.90","7.17","6.05","6.43"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.46","1.06","1.00","1.32","1.27","0.95","1.06"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[21,46,40,53,51,41,43],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[0,3,6,8,8,3,6],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0,4535,3135,3585,3589,4218,5739],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","97.89","67.67","77.33","77.37","91.03","123.88"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["98.451","99.498","99.483","99.664","99.748","99.432","99.584"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.001","1.002","1.002","1.002","1.002","1.003","1.001"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4399 + 32 part","4467 + 14 part","4465 + 13 part","4476 + 11 part","4477 + 11 part","4467 + 11 part","4470 + 13 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[285889,1039305,1039501,1039458,1548245,1548139,1745314],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[133059,2497845,1238868,2501081,3194637,1238635,3392211],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[78649,327068,425744,302458,326982,366279,367606],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[139864,571664,425173,852639,1039467,1039472,1039654],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[78649,302440,269982,302440,285889,285889,302456],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[133059,571664,425173,852639,1039467,1039472,1039654],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[78649,302440,269982,302440,285889,285889,302456],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[12,1,2,1,1,2,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[22,3,4,3,2,3,2],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[11,3,3,3,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[22,6,7,5,5,5,4],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[12,3,3,3,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[22,6,7,5,5,5,4],"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":["spd_miseq","spd_sspace_1cell","spd_sspace_2cell","spd_sspace_3cell","spd_sspace_4cell","spd_sspace_17cell","spd_sspace_p4c2"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"spd_sspace_p4c2":[3324,335,270,247,171,121,0,2,0,0,0,0,0,0],"spd_sspace_4cell":[3116,343,278,269,171,121,116,60,3,0,0,0,0,0,0],"spd_miseq":[270,240,265,206,212,191,221,175,171,141,120,122,119,113,101,102,112,95,83,89,96,73,60,57,57,51,54,54,56,44,37,60,42,42,31,38,41,29,38,28,37,19,25,27,30,14,18,11,7,8,13,9,0,7,7,4,2,5,1,2,2,3,2,1,2,1,2,1,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0],"spd_sspace_17cell":[1889,1229,333,270,206,203,171,121,44,1,0,0,0,0,0,0,0],"spd_sspace_1cell":[2442,675,308,278,206,171,121,114,92,60,0,0,0,0,0],"spd_sspace_2cell":[1216,1225,541,406,335,203,171,120,114,92,41,0,1,0,0,0,0,0],"spd_sspace_3cell":[2445,882,278,270,171,121,137,113,59,0,0,0,0,0,0,0]},"filenames":["spd_miseq","spd_sspace_1cell","spd_sspace_2cell","spd_sspace_3cell","spd_sspace_4cell","spd_sspace_17cell","spd_sspace_p4c2"]}
{{ 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.