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":"25 July 2014, Friday, 13:56:29","report":[["Statistics without reference",[{"values":[31,57,32,79,29],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[31,57,32,79,29],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[31,57,32,79,29],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[3188995,3186675,1674993,263863,2634704],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4592561,4583750,4620837,4096056,4628207],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4592561,4583750,4620837,4096056,4628207],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4592561,4583750,4620837,4096056,4628207],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[3188995,3186675,1492665,99916,2634704],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[904060,941271,915131,75373,296653],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,2,14,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[2,2,3,25,4],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["68.78","68.79","68.67","67.12","68.70"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[6,4,10,249,16],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[2,1,3,224,12],"quality":"Less is better","isMain":false,"metricName":" # 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both parts are significant"},{"values":[0,0,0,13329,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[266,192,339,631,318],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[167,162,206,144,226],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[562,388,687,630,1332],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["5.81","4.23","7.41","21.37","7.02"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["3.65","3.57","4.50","4.88","4.99"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[152,150,181,129,192],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[15,12,25,15,34],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[5545,6844,9142,1118657,72783],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["120.74","149.31","197.84","27310.59","1572.60"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.417","98.669","99.437","64.402","98.348"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.004","1.009","1.010","1.378","1.022"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4345 + 30 part","4308 + 47 part","4341 + 31 part","2162 + 1205 part","4183 + 185 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[3182258,3180491,1671977,109429,1195625],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[3188995,3186675,1492665,93493,2634704],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[904060,941271,915131,65785,296653],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[3182258,3180491,1486855,14496,511933],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[733985,933753,903997,null,125717],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[3182258,3180491,1486855,9775,511933],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[733985,933753,903997,null,125717],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,2,16,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[2,2,3,31,4],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1,1,2,74,3],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[2,2,3,null,8],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1,1,2,95,3],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[2,2,3,null,8],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4603060,4603060,4603060,4603060,4603060],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["68.79","68.79","68.79","68.79","68.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4388,4388,4388,4388,4388],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4],"assembliesNames":["alg_d2_web_nopac","alg_d2_raw_nopac","alg_d2_frac_nopac","alg_d2_50X_nopac","alg_d2_100X_nopac"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":4603060}
{"ref_genes_number":4388,"genes_in_contigs":{"alg_d2_web_nopac":[3099,820,101,47,40,41,40,27,27,21,17,17,9,11,6,6,3,3,0,2,0,3,1,1,1,1,0,0,0,0,1],"alg_d2_raw_nopac":[3095,859,101,61,24,27,3,16,11,9,11,6,11,8,5,5,7,5,3,2,3,4,2,0,3,1,3,2,2,0,1,2,2,1,0,1,1,3,1,2,1,0,0,0,0,2,1,0,0,0,0,0,0,0,0,1,0],"alg_d2_50X_nopac":[154,108,122,95,88,92,110,99,62,55,46,46,56,45,41,34,32,40,55,46,39,54,50,34,34,25,29,34,26,39,33,31,27,40,22,27,17,14,19,19,24,10,3,6,11,4,8,3,9,6,7,9,2,2,3,2,3,0,1,2,1,0,1,0,0,1,0,1,0,1,1,0,0,1,1,0,0,0,0],"alg_d2_100X_nopac":[2426,457,286,237,265,117,99,89,42,34,34,22,5,10,11,10,12,7,6,8,2,0,1,1,0,0,1,0,1],"alg_d2_frac_nopac":[1607,1466,816,100,61,35,41,44,40,22,17,23,0,17,10,9,11,6,5,3,3,1,0,2,1,0,0,0,0,0,0,1]},"filenames":["alg_d2_web_nopac","alg_d2_raw_nopac","alg_d2_frac_nopac","alg_d2_50X_nopac","alg_d2_100X_nopac"]}
{{ 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.