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, 11:54:14","report":[["Statistics without reference",[{"values":[2,8,10,14,1,1,4],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[2,8,10,14,1,1,4],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[2,8,10,14,1,1,4],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[4278957,2277010,1213670,984459,4641350,4640250,3162440],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4650771,4648304,4644602,4656274,4641350,4640250,4653394],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4650771,4648304,4644602,4656274,4641350,4640250,4653394],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4650771,4648304,4644602,4656274,4641350,4640250,4653394],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[4278957,622425,800993,565251,4641350,4640250,3162440],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[4278957,438633,721189,260663,4641350,4640250,1074537],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,2,3,4,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,4,4,6,1,1,2],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.79","50.84","50.83","50.84","50.80","50.80","50.80"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[9,9,9,8,8,8,9],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[8,8,8,8,7,7,8],"quality":"Less is better","isMain":false,"metricName":" # 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with misassembly"},{"values":[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],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[17,115,87,249,32,31,40],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[166,2468,2119,3380,494,523,485],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[188,2698,2325,3643,548,598,539],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.37","2.49","1.88","5.38","0.69","0.67","0.86"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["3.58","53.34","45.82","73.07","10.65","11.28","10.46"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[166,2468,2119,3379,494,523,485],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[0,0,0,1,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0,2,1,4,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.04","0.02","0.09","0.00","0.00","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.993","99.733","99.670","99.693","99.972","99.946","99.968"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.002","1.005","1.006","1.007","1.001","1.001","1.003"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4492 + 5 part","4475 + 10 part","4467 + 12 part","4469 + 13 part","4492 + 4 part","4491 + 4 part","4492 + 4 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[1075711,957980,800993,949468,1926702,1927324,1074537],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[4278957,622425,800993,565251,4641350,4640250,3162440],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[4278957,438633,721189,260663,4641350,4640250,1074537],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[859464,621281,572455,436292,1098529,1096784,859502],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[727685,297470,420796,209024,949340,949325,686825],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[859464,621281,572455,436292,1098529,1096784,859502],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[727685,297470,420796,209024,949340,949325,686825],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,2,3,4,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,4,4,6,1,1,2],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[3,3,4,4,2,2,3],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[4,6,6,8,3,3,4],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[3,3,4,4,2,2,3],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[4,6,6,8,3,3,4],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[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"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497,4497,4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4,5,6],"assembliesNames":["pbcr_d6_all","pbcr_d6_rg4_1","pbcr_d6_rg4_2","pbcr_d6_rg4_3","pbcr_d6_rg6_1","pbcr_d6_rg6_2","pbcr_d6_rg6_3"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"pbcr_d6_rg4_1":[2189,569,555,426,351,172,131,82],"pbcr_d6_rg4_2":[1167,888,772,669,399,195,136,117,90,34],"pbcr_d6_rg4_3":[968,597,649,518,441,260,213,202,181,155,131,53,56,45],"pbcr_d6_all":[4150,342],"pbcr_d6_rg6_2":[4491],"pbcr_d6_rg6_3":[3065,1041,347,39],"pbcr_d6_rg6_1":[4492]},"filenames":["pbcr_d6_all","pbcr_d6_rg4_1","pbcr_d6_rg4_2","pbcr_d6_rg4_3","pbcr_d6_rg6_1","pbcr_d6_rg6_2","pbcr_d6_rg6_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.