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, 13:59:52","report":[["Statistics without reference",[{"values":[1,3,3,3],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[1,3,3,3],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[1,3,3,3],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[5163983,2232679,2236613,2237949],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[5163983,5161276,5165518,5166563],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[5163983,5161276,5165518,5166563],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[5163983,5161276,5165518,5166563],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[5163983,2043590,2044147,2135225],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[5163983,2043590,2044147,2135225],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,2,2,2],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,2,2,2],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["42.05","42.04","42.05","42.05"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[0,0,0,0],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[0,0,0,0],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[434,514,427,531],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[113,980,678,723],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[133,1142,728,781],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["8.41","9.96","8.27","10.29"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["2.19","18.99","13.13","14.01"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[113,979,678,723],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[0,1,0,0],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.00","0.00","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.919","99.864","99.907","99.890"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.000","1.000","1.001","1.001"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4335 + 3 part","4330 + 5 part","4333 + 5 part","4333 + 3 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[5163983,2232679,2236613,2237949],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[5163983,2043590,2044147,2135225],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[5163983,2043590,2044147,2135225],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[5163983,2043590,2044147,2135225],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[5163983,2043590,2044147,2135225],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[5163983,2043590,2044147,2135225],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[5163983,2043590,2044147,2135225],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[1,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[1,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[5167383,5167383,5167383,5167383],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["42.05","42.05","42.05","42.05"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4339,4339,4339,4339],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3],"assembliesNames":["pbcr_d8_all","pbcr_d8_rg4_1","pbcr_d8_rg4_2","pbcr_d8_rg4_3"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[5163983],[2232679,2043590,885007],[2236613,2044147,884758],[2237949,2135225,793389]],"filenames":["pbcr_d8_all","pbcr_d8_rg4_1","pbcr_d8_rg4_2","pbcr_d8_rg4_3"]}
{"lists_of_lengths":[[5163983],[2232679,2043590,885007],[2236613,2044147,884758],[2237949,2135225,793389]],"filenames":["pbcr_d8_all","pbcr_d8_rg4_1","pbcr_d8_rg4_2","pbcr_d8_rg4_3"]}
{"assemblies_lengths":[5163983,5161276,5165518,5166563],"filenames":["pbcr_d8_all","pbcr_d8_rg4_1","pbcr_d8_rg4_2","pbcr_d8_rg4_3"]}
{"reflen":5167383}
{"ref_genes_number":4339,"genes_in_contigs":{"pbcr_d8_rg4_1":[1868,1665,797],"pbcr_d8_rg4_3":[1872,1747,714],"pbcr_d8_all":[4335],"pbcr_d8_rg4_2":[1871,1665,797]},"filenames":["pbcr_d8_all","pbcr_d8_rg4_1","pbcr_d8_rg4_2","pbcr_d8_rg4_3"]}
{{ 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.