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, 16:42:00","report":[["Statistics without reference",[{"values":[19,24,21,28,38,29,31],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[19,24,21,28,38,29,31],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[19,24,21,28,38,29,31],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[745120,664876,562203,663399,434084,345313,437164],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4669108,4675696,4700617,4636263,4644391,4603072,4578972],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4669108,4675696,4700617,4636263,4644391,4603072,4578972],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4669108,4675696,4700617,4636263,4644391,4603072,4578972],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[356974,222559,399011,295449,180706,207976,191458],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[192819,173421,220527,137921,111284,143023,127979],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[5,5,5,6,9,9,8],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[10,11,9,12,18,16,15],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.78","50.81","50.75","50.79","50.82","50.84","50.77"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[8,6,12,8,7,8,6],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[8,6,11,8,7,8,5],"quality":"Less is better","isMain":false,"metricName":" # 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with misassembly"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[127,127,141,325,269,404,168],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[99,39,46,558,199,111,97],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[140,62,63,694,290,130,206],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["2.75","2.75","3.04","7.08","5.85","8.82","3.69"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["2.14","0.84","0.99","12.15","4.33","2.42","2.13"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[95,37,45,553,196,111,91],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[4,2,1,5,3,0,6],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[9,1,2,12,7,3,1],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.19","0.02","0.04","0.26","0.15","0.07","0.02"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.639","99.699","99.834","98.984","99.051","98.780","98.159"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.010","1.011","1.015","1.011","1.011","1.005","1.005"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4473 + 15 part","4465 + 18 part","4480 + 10 part","4435 + 29 part","4431 + 36 part","4413 + 36 part","4380 + 34 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[626989,615169,560495,436657,366520,295236,437162],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[356974,222559,399011,295449,180706,207976,191458],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[192819,173421,220527,137921,111284,143023,116843],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[356957,221098,278640,226118,179662,194634,191457],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[179177,129844,161912,119418,111284,131997,127979],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[356957,221098,278640,226118,179662,194634,191457],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[179177,172210,161912,119418,111284,131997,112837],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[5,5,5,6,9,9,8],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[10,11,9,12,18,16,16],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[5,6,6,7,10,10,8],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[11,12,11,14,19,18,15],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[5,6,6,7,10,10,8],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[11,11,11,14,19,18,16],"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":["071634_raw_asm.ctg","192221_raw_asm.ctg","210845_raw_asm.ctg","071634_100X_asm.ctg","071634_118X_asm.ctg","192221_118X_asm.ctg","210845_118X_asm.ctg"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"192221_118X_asm.ctg":[361,356,279,291,251,199,206,203,184,203,174,142,150,142,137,131,120,111,114,106,86,77,99,89,59,37,35,32,39],"071634_118X_asm.ctg":[457,335,270,265,207,217,203,189,172,175,142,157,116,112,105,101,98,107,98,89,75,75,64,65,59,57,44,43,55,36,46,37,39,38,26,32,19,6],"071634_raw_asm.ctg":[745,654,394,363,348,215,183,175,197,204,172,138,114,114,129,121,94,72,41],"192221_raw_asm.ctg":[657,595,592,264,198,204,232,181,187,180,146,116,108,124,94,95,77,83,79,67,60,64,38,24],"210845_raw_asm.ctg":[512,507,446,499,401,314,256,257,223,164,140,119,91,100,116,70,84,63,45,37,36],"071634_100X_asm.ctg":[658,409,347,338,328,279,204,201,172,175,139,128,105,120,95,89,96,74,106,73,57,45,34,37,42,34,28,22],"210845_118X_asm.ctg":[409,372,335,251,245,225,190,202,163,157,171,143,136,120,114,130,108,107,113,95,88,89,97,61,57,40,37,30,38,39,18]},"filenames":["071634_raw_asm.ctg","192221_raw_asm.ctg","210845_raw_asm.ctg","071634_100X_asm.ctg","071634_118X_asm.ctg","192221_118X_asm.ctg","210845_118X_asm.ctg"]}
{{ 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.