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, 17:05:12","report":[["Statistics without reference",[{"values":[34,56,11,19,7,16,5,7],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[34,56,11,19,7,16,5,7],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[34,56,11,19,7,16,5,7],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[762617,578194,1341765,694845,2069213,1204169,2021284,1754178],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4798555,4933914,4612517,4629273,4635310,4744173,4666475,4690899],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4798555,4933914,4612517,4629273,4635310,4744173,4666475,4690899],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4798555,4933914,4612517,4629273,4635310,4744173,4666475,4690899],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[412414,318728,1155479,498347,1478089,678445,1215597,1253429],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[220464,90544,652602,191279,1478089,289684,650640,676150],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[4,6,2,4,2,3,2,2],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[8,15,4,8,2,6,3,3],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.75","50.86","50.76","50.76","50.79","50.79","50.79","50.80"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[9,8,8,12,10,8,8,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[8,8,7,11,9,7,7,7],"quality":"Less is better","isMain":false,"metricName":" # 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long indels"},{"values":[7,2,0,0,0,4,1,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.15","0.04","0.00","0.00","0.00","0.08","0.02","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.769","99.515","99.189","98.957","99.561","99.985","99.944","100.000"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.037","1.070","1.002","1.008","1.003","1.023","1.006","1.011"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4479 + 13 part","4469 + 14 part","4465 + 12 part","4454 + 15 part","4467 + 12 part","4491 + 6 part","4487 + 6 part","4492 + 5 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[762616,578194,949312,694845,1477214,1204161,2021279,1753969],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[412414,318728,1155479,460790,1478089,678445,1215597,1253429],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[220464,108511,652602,191279,1478089,383368,650640,676150],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[368011,218575,694825,340107,1392456,496729,768685,834919],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[180996,86548,270104,191279,670145,198833,446144,325599],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[368011,230980,694825,340107,1392456,496729,768685,834919],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[189541,102337,270104,191279,670145,256261,446144,421309],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[4,6,2,5,2,3,2,2],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[8,13,4,8,2,5,3,3],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[5,8,3,5,2,3,2,2],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[9,17,6,9,3,7,4,5],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[5,7,3,5,2,3,2,2],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[8,15,6,9,3,6,4,4],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675,4639675,4639675,4639675,4639675,4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79","50.79","50.79","50.79","50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497,4497,4497,4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4,5,6,7],"assembliesNames":["wo_all_runCA1","wo_all_runCA2","wo_25X_runCA1","wo_25X_runCA2","w_all_runCA1","w_all_runCA2","w_25X_runCA1","w_25X_runCA2"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"wo_25X_runCA1":[1320,1127,680,604,203,171,114,88,89,33,36],"w_all_runCA2":[1168,693,688,466,352,288,146,117,100,84,91,74,75,49,65,35],"w_all_runCA1":[2023,1393,633,153,127,106,32],"wo_25X_runCA2":[680,575,467,513,445,337,261,203,171,137,111,114,106,89,73,43,54,39,36],"w_25X_runCA2":[1686,1210,672,462,260,153,49],"w_25X_runCA1":[1938,1170,613,423,343],"wo_all_runCA1":[735,622,619,408,340,328,269,228,173,118,108,128,89,75,58,34,38,37,20,25,8,0,0,4,0,1,8,0,2,2,0,1,1,0],"wo_all_runCA2":[535,532,405,341,330,318,222,177,144,120,106,107,109,84,88,65,70,65,61,67,64,67,53,41,38,32,37,26,22,24,23,16,16,1,3,10,1,1,7,14,7,1,3,5,0,5,0,1,0,0,0,0,0,2,3,0]},"filenames":["wo_all_runCA1","wo_all_runCA2","wo_25X_runCA1","wo_25X_runCA2","w_all_runCA1","w_all_runCA2","w_25X_runCA1","w_25X_runCA2"]}
{{ 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.