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, 16:04:32","report":[["Statistics without reference",[{"values":[20,90],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[71,3109],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[18,19],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[433183,423414],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[2157030,2239813],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[2165872,3047071],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[2155724,2195271],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[210016,365564],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[104024,208537],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[4,3],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[8,5],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["39.57","39.80"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[13,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[12,7],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[6,2],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[1358992,815978],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[30,19],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,73],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,57455],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,2],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,1059],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[566,675],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[96,62],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[260,215],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["26.66","31.50"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["4.52","2.89"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[82,52],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[14,10],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[15686,9293],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["727.20","414.90"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["98.267","99.177"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.017","1.018"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["2244 + 25 part","2269 + 21 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[405380,364006],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[210016,365564],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[104024,208537],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[124123,208537],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[83766,119029],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[124123,208537],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[83766,119029],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[4,3],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[8,5],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[5,4],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[11,8],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[5,4],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[11,8],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[2160842,2160842],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["39.70","39.70"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[2301,2301],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1],"assembliesNames":["spd_d3_web","spd_d3_raw"]}
{{ qualities }}
{{ mainMetrics }}
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{"assemblies_lengths":[2157030,2239813],"filenames":["spd_d3_web","spd_d3_raw"]}
{"reflen":2160842}
{"ref_genes_number":2301,"genes_in_contigs":{"spd_d3_web":[446,246,243,223,182,130,145,112,102,120,89,74,76,43,7,5,1,0,0,0],"spd_d3_raw":[441,411,376,313,189,146,132,102,74,79,0,0,4,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]},"filenames":["spd_d3_web","spd_d3_raw"]}
{{ 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],[0,0,0,0,0,0,0,0,0,0,0,1,0,0,2,3,4,5,13,19,36,46,84,77,147,154,227,276,320,369,438,560,635,680,699,854,921,1003,1133,1178,1270,1254,1290,1262,1168,1133,922,860,663,526,389,286,191,107,78,46,45,15,11,6,3,3,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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],[0,0,0,0,0,0,0,0,0,0,0,1,1,0,1,2,2,6,10,26,33,56,63,117,116,145,249,281,302,411,446,533,644,752,751,867,922,1018,1178,1194,1216,1314,1327,1348,1223,1132,1032,817,747,551,404,307,224,160,113,93,56,40,23,13,14,7,4,5,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null,"filenames":["spd_d3_web","spd_d3_raw"]}
{
"# 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.