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, 15:44:19","report":[["Statistics without reference",[{"values":[57,44],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[145,5063],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[49,36],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[1209840,1895290],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4566203,4584163],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4575425,4928179],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4559895,4578264],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[318530,422736],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[149621,189839],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[3,2],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[9,7],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["68.81","68.81"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[33,10],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[15,3],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[14,7],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[4,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[12,7],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[3312932,1235058],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[116,49],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[3,1],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[1,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[2031,22],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[2426,1722],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[1052,366],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[4107,780],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["53.46","37.73"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["23.18","8.02"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[966,348],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[86,18],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[9425,3662],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["206.41","79.88"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["98.589","99.157"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.006","1.005"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4170 + 166 part","4287 + 68 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[501014,1892377],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[318530,422736],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[149621,189839],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[164917,331154],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[92560,189662],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[164917,331154],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[92560,189662],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[3,2],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[9,7],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[9,3],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[18,7],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[9,3],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[18,7],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4603060,4603060],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["68.79","68.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4388,4388],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1],"assembliesNames":["spd_d2_web","spd_d2_raw"]}
{{ qualities }}
{{ mainMetrics }}
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{"lists_of_lengths":[[501014,364653,317718,278814,228734,197757,176798,168013,164917,156931,148828,134006,125874,114299,109357,105291,104526,92560,90665,86110,82611,73798,71298,67588,60636,53701,43770,40163,34065,29179,28201,28104,24693,21373,20268,19397,18481,12418,10750,10018,9772,8556,8481,7345,6962,5350,5300,5047,4902,4450,4280,4011,3924,3746,3210,2841,2592,2571,2570,2464,2180,1985,1947,1834,1627,1577,1575,1472,1449,1383,1318,1246,1167,1148,1095,921,899,869,819,775,744,717,698,671,558,505,407,401,352,326],[1892377,393665,331154,266177,218743,215018,189662,124412,112630,103776,97340,86626,81857,68641,60593,57287,37561,36188,28204,24818,17240,16682,14489,12358,10231,9111,7098,6136,5491,5350,4877,4810,4486,4159,3201,2942,2755,2214,1627,1606,1433,1317,1218,1101,1091,1072,966,921,917,813,648,564,554,516]],"filenames":["spd_d2_web","spd_d2_raw"]}
{"assemblies_lengths":[4566203,4584163],"filenames":["spd_d2_web","spd_d2_raw"]}
{"reflen":4603060}
{"ref_genes_number":4388,"genes_in_contigs":{"spd_d2_raw":[1804,381,409,249,206,212,177,105,102,100,88,100,95,56,46,41,33,16,25,12,7,5,6,2,2,0,0,2,1,0,1,0,0,0,0,1,1,2,0,0,0,0,0,0],"spd_d2_web":[1098,886,283,196,177,162,148,153,134,109,121,100,105,89,84,61,33,38,38,33,23,18,8,10,10,11,3,4,5,3,2,3,2,3,1,1,0,1,3,2,1,0,0,2,1,0,0,1,0,2,0,0,0,1,1,0,0]},"filenames":["spd_d2_web","spd_d2_raw"]}
{{ 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.