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, 13:57:27","report":[["Statistics without reference",[{"values":[2],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[2974307],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[3100289],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[3100289],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[3100289],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[2974307],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[2974307],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["63.38"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[2],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[2],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[2974307],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[7],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[155],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[172],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.23"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["5.01"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[154],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.03"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.883"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.002"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["3093 + 4 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[1707938],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[2974307],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[2974307],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[1707938],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[1265012],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[1707938],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[1265012],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[2],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[2],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[3097457],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["63.38"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[3105],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0],"assembliesNames":["pbcr_d7_all"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[2974307,125982]],"filenames":["pbcr_d7_all"]}
{"lists_of_lengths":[[1707938,1265012,125982,1277]],"filenames":["pbcr_d7_all"]}
{"assemblies_lengths":[3100289],"filenames":["pbcr_d7_all"]}
{"reflen":3097457}
{"ref_genes_number":3105,"genes_in_contigs":{"pbcr_d7_all":[2976,117]},"filenames":["pbcr_d7_all"]}
{{ operonsInContigs }}
{"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,1,3,3,2,5,3,8,16,17,16,27,33,35,36,58,99,98,136,184,223,268,309,385,445,575,697,798,986,1099,1277,1470,1597,1782,1916,1986,1919,1978,1890,1689,1560,1348,1099,846,686,498,349,222,145,84,41,32,12,8,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null,"filenames":["pbcr_d7_all"]}
{
"# 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.