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, 16:02:26","report":[["Statistics without reference",[{"values":[2,6,1,4,2,4,2,3,2],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[2,6,1,4,2,4,2,3,2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[2,6,1,4,2,4,2,3,2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[3768995,4105501,4644254,3784001,4646000,3287004,4646998,4622502,4647000],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4649500,4678503,4644254,4660999,4655498,4667500,4660992,4660836,4656000],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4649500,4678503,4644254,4660999,4655498,4667500,4660992,4660836,4656000],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4649500,4678503,4644254,4660999,4655498,4667500,4660992,4660836,4656000],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[3768995,4105501,4644254,3784001,4646000,3287004,4646998,4622502,4647000],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[3768995,4105501,4644254,3784001,4646000,1096995,4646998,4622502,4647000],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,1,1,1,1,2,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.80","50.76","50.79","50.79","50.78","50.79","50.77","50.79","50.78"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[8,10,10,9,8,8,8,9,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[7,9,9,8,7,7,7,8,7],"quality":"Less is better","isMain":false,"metricName":" # 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with misassembly"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[7,23,17,9,5,5,6,10,8],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[15,128,10,67,23,27,9,62,22],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[17,148,16,72,27,29,11,66,25],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.15","0.50","0.37","0.19","0.11","0.11","0.13","0.22","0.17"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.32","2.76","0.22","1.44","0.50","0.58","0.19","1.34","0.47"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[15,128,10,67,23,27,9,62,22],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.00","0.00","0.00","0.00","0.00","0.00","0.00","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["100.000","100.000","99.994","99.999","100.000","100.000","100.000","99.990","100.000"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.002","1.008","1.001","1.005","1.003","1.006","1.005","1.005","1.004"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4494 + 3 part","4494 + 3 part","4493 + 3 part","4493 + 4 part","4495 + 2 part","4495 + 2 part","4495 + 2 part","4493 + 4 part","4495 + 2 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[1295052,3026413,1555879,3026418,3026418,1096995,2126982,1947376,2674710],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[3768995,4105501,4644254,3784001,4646000,3287004,4646998,4622502,4647000],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[3768995,4105501,4644254,3784001,4646000,1096995,4646998,4622502,4647000],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[880505,3026413,949310,3026418,3026418,980837,1041003,1059045,2674710],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[857866,942635,691071,659459,949288,690082,903935,949310,949310],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[880505,3026413,949310,3026418,3026418,980837,1041003,1059045,2674710],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[857866,942635,691071,659459,949288,690082,903935,949310,949310],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,1,1,1,1,2,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[3,1,2,1,1,3,2,2,1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[4,2,4,2,2,4,3,3,2],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[3,1,2,1,1,3,2,2,1],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[4,2,4,2,2,4,3,3,2],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675,4639675,4639675,4639675,4639675,4639675,4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79","50.79","50.79","50.79","50.79","50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497,4497,4497,4497,4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4,5,6,7,8],"assembliesNames":["hgap_d5_rg4_1","hgap_d5_rg4_2","hgap_d5_rg4_3","hgap_d5_rg6_1","hgap_d5_rg6_2","hgap_d5_rg6_3","hgap_d5_rg8_1","hgap_d5_rg8_2","hgap_d5_rg8_3"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[3768995,880505],[4105501,522002,15490,12499,11507,11504],[4644254],[3784001,668501,195998,12499],[4646000,9498],[3287004,1096995,271500,12001],[4646998,13994],[4622502,22498,15836],[4647000,9000]],"filenames":["hgap_d5_rg4_1","hgap_d5_rg4_2","hgap_d5_rg4_3","hgap_d5_rg6_1","hgap_d5_rg6_2","hgap_d5_rg6_3","hgap_d5_rg8_1","hgap_d5_rg8_2","hgap_d5_rg8_3"]}
{"lists_of_lengths":[[1295052,949289,880505,857866,572343,89891,1818,1199,769,768],[3026413,942635,438122,134916,82676,14684,11504,10301,5060,4629,2198,1818,1204,806,769,768],[1555879,949310,742849,691071,572340,89875,38374,1818,1201,769,768],[3026418,659459,464781,291265,107519,87279,9846,7224,2653,1818,1200,769,768],[3026418,949288,409992,165857,89891,9496,1818,1199,769,768],[1096995,1041004,980837,690082,572340,271500,5118,5060,1818,1201,769,768],[2126982,1041003,903935,572340,7112,5064,1818,1201,769,768],[1947376,1059045,949310,572340,89874,22498,11539,4156,1818,1201,769,768],[2674710,949310,572340,356210,89874,9000,1818,1201,769,768]],"filenames":["hgap_d5_rg4_1","hgap_d5_rg4_2","hgap_d5_rg4_3","hgap_d5_rg6_1","hgap_d5_rg6_2","hgap_d5_rg6_3","hgap_d5_rg8_1","hgap_d5_rg8_2","hgap_d5_rg8_3"]}
{"assemblies_lengths":[4649500,4678503,4644254,4660999,4655498,4667500,4660992,4660836,4656000],"filenames":["hgap_d5_rg4_1","hgap_d5_rg4_2","hgap_d5_rg4_3","hgap_d5_rg6_1","hgap_d5_rg6_2","hgap_d5_rg6_3","hgap_d5_rg8_1","hgap_d5_rg8_2","hgap_d5_rg8_3"]}
{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"hgap_d5_rg6_2":[4494,1],"hgap_d5_rg6_3":[3199,1047,249,0],"hgap_d5_rg6_1":[3647,656,190,0],"hgap_d5_rg4_1":[3627,867],"hgap_d5_rg4_2":[3952,515,11,1,12,3],"hgap_d5_rg4_3":[4493],"hgap_d5_rg8_1":[4495,0],"hgap_d5_rg8_2":[4472,21,0],"hgap_d5_rg8_3":[4494,1]},"filenames":["hgap_d5_rg4_1","hgap_d5_rg4_2","hgap_d5_rg4_3","hgap_d5_rg6_1","hgap_d5_rg6_2","hgap_d5_rg6_3","hgap_d5_rg8_1","hgap_d5_rg8_2","hgap_d5_rg8_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.