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, 16:59:20","report":[["Statistics without reference",[{"values":[17,6,10],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[17,6,10],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[17,6,10],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[1214624,1487482,2034167],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4691318,4671508,4678847],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4691318,4671508,4678847],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4691318,4671508,4678847],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[672326,1340503,907105],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[298900,819567,367279],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[3,2,2],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[6,3,4],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.82","50.81","50.79"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[10,6,10],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[9,6,9],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[1,0,1],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[3,3,4],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[1424020,2055756,3075921],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[8,8,5],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[331,280,303],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[72,31,59],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[78,119,140],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["7.13","6.05","6.53"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["1.55","0.67","1.27"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[72,26,56],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[0,5,3],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0,3,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.06","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.997","99.824","99.961"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.011","1.009","1.010"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4488 + 9 part","4485 + 4 part","4491 + 4 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[1214360,1340503,1257634],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[672326,1340503,907105],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[298900,819567,367279],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[315240,1008667,572351],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[194843,477952,367175],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[315240,1008667,572351],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[194843,477952,367175],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[3,2,2],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[6,3,4],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[4,2,3],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[9,4,5],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[4,2,3],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[9,4,5],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2],"assembliesNames":["2_25X_asm.ctg","3_25X_asm.ctg","4_25X_asm.ctg"]}
{{ qualities }}
{{ mainMetrics }}
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{"lists_of_lengths":[[1214360,520713,367128,315240,298900,238793,237544,197118,194843,182079,151406,135509,112813,96680,95401,89875,65058,50204,46294,35523,31288,9343,1818,1204,769,768,378],[1340503,1008667,819567,477952,455682,248597,125021,96699,95815,1200,769,769],[1257634,848123,572351,529499,367175,362943,183072,110505,100617,89893,82142,58982,56496,32725,17203,1818,1794,1198,768,768]],"filenames":["2_25X_asm.ctg","3_25X_asm.ctg","4_25X_asm.ctg"]}
{"assemblies_lengths":[4691318,4671508,4678847],"filenames":["2_25X_asm.ctg","3_25X_asm.ctg","4_25X_asm.ctg"]}
{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"4_25X_asm.ctg":[1998,845,511,359,327,175,96,67,55,58],"3_25X_asm.ctg":[1456,1277,786,422,343,201],"2_25X_asm.ctg":[1157,690,677,337,308,276,206,173,139,120,98,90,70,35,38,51,23]},"filenames":["2_25X_asm.ctg","3_25X_asm.ctg","4_25X_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.