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, 11:56:42","report":[["Statistics without reference",[{"values":[1],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[4656257],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4656257],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4656257],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4656257],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[4656257],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[4656257],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.76"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[7],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[4656257],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[2],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[10],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[610],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[615],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.22"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["13.15"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[610],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["100.000"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.004"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4494 + 3 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[3026094],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[4656257],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[4656257],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[3026094],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[949166],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[3026094],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[949166],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[2],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[2],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0],"assembliesNames":["pbcr_d9_all"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[4656257]],"filenames":["pbcr_d9_all"]}
{"lists_of_lengths":[[3026094,949166,572310,91518,12615,1818,1199,769,768]],"filenames":["pbcr_d9_all"]}
{"assemblies_lengths":[4656257],"filenames":["pbcr_d9_all"]}
{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"pbcr_d9_all":[4494]},"filenames":["pbcr_d9_all"]}
{{ operonsInContigs }}
{"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,6,11,8,10,17,31,33,60,64,75,98,140,159,168,208,237,282,319,348,405,437,522,658,731,842,978,1217,1362,1587,1811,2179,2330,2599,2819,2989,2859,2917,2764,2573,2141,1898,1535,1194,879,652,490,334,230,140,68,57,31,22,17,4,6,2,1,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null,"filenames":["pbcr_d9_all"]}
{
"# 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.