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, 11:51:28","report":[["Statistics without reference",[{"values":[1,1,1,5,2,2,1,4,1,2],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[1,1,1,5,2,2,1,4,1,2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[1,1,1,5,2,2,1,4,1,2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[4651604,4647117,4648057,3447068,3749516,2770859,4649699,1679082,4649323,4189785],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4651604,4647117,4648057,4661453,4645941,4657272,4649699,4655949,4649323,4652482],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4651604,4647117,4648057,4661453,4645941,4657272,4649699,4655949,4649323,4652482],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4651604,4647117,4648057,4661453,4645941,4657272,4649699,4655949,4649323,4652482],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[4651604,4647117,4648057,3447068,3749516,2770859,4649699,1159845,4649323,4189785],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[4651604,4647117,4648057,656513,3749516,1886413,4649699,983561,4649323,4189785],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,1,1,1,1,2,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,1,1,2,1,2,1,3,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.79","50.79","50.79","50.80","50.78","50.77","50.78","50.79","50.78","50.79"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[9,9,8,9,7,9,10,7,10,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[8,8,7,8,7,9,8,7,8,7],"quality":"Less is better","isMain":false,"metricName":" # 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{{ qualities }}
{{ mainMetrics }}
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{"lists_of_lengths":[[2834925,949285,572340,198539,89891,1819,1818,1199,769,768],[1219471,958747,949217,852958,572285,89885,1818,1199,769,768],[2172149,949242,859936,572305,89869,1818,1201,769,768],[1185186,949257,656513,611492,572322,374632,138151,89882,45089,34372,1817,1204,768,768],[2796469,949042,572328,232186,89895,3236,1204,769,769],[2139084,1040965,624295,572325,236035,34351,5331,1808,1200,769,768],[3026388,949281,572334,89891,4673,1818,1818,1199,769,768,760],[1677251,949298,833461,572339,495643,89673,33395,1195,769,769,99],[3027267,949279,572334,89874,3416,1819,1818,1199,780,769,768],[1717391,949289,856349,572328,462657,89872,1818,1201,769,768]],"filenames":["pbcr_d5_all","pbcr_d5_rg4_1","pbcr_d5_rg4_2","pbcr_d5_rg4_3","pbcr_d5_rg6_1","pbcr_d5_rg6_2","pbcr_d5_rg6_3","pbcr_d5_rg8_1","pbcr_d5_rg8_2","pbcr_d5_rg8_3"]}
{"assemblies_lengths":[4651604,4647117,4648057,4661453,4645941,4657272,4649699,4655949,4649323,4652482],"filenames":["pbcr_d5_all","pbcr_d5_rg4_1","pbcr_d5_rg4_2","pbcr_d5_rg4_3","pbcr_d5_rg6_1","pbcr_d5_rg6_2","pbcr_d5_rg6_3","pbcr_d5_rg8_1","pbcr_d5_rg8_2","pbcr_d5_rg8_3"]}
{"reflen":4639675}
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{{ 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.