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, 11:46:49","report":[["Statistics without reference",[{"values":[2,1,5,3,2],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[2,1,5,3,2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[2,1,5,3,2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[4631220,4633080,4575759,4629108,4638312],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4633146,4633080,4698903,4633082,4640072],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4633146,4633080,4698903,4633082,4640072],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4633146,4633080,4698903,4633082,4640072],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[4631220,4633080,4575759,4629108,4638312],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[4631220,4633080,4575759,4629108,4638312],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.76","50.75","50.72","50.76","50.76"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[3,7,8,8,5],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[3,7,7,7,5],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,1,1,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1,1,2,2,1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[4631220,4633080,4577746,4631095,4638312],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[29,66,32,30,34],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[55,65,131,116,104],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[19,24,33,22,24],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[208,423,219,185,332],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["1.19","1.42","2.84","2.52","2.26"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.41","0.53","0.72","0.48","0.52"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[13,8,25,16,15],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[6,16,8,6,9],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[24705,71582,32839,32615,35282],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["533.22","1545.02","698.87","703.96","760.38"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.345","98.343","99.265","99.136","99.272"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.005","1.016","1.021","1.008","1.008"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4465 + 11 part","4395 + 31 part","4460 + 14 part","4451 + 13 part","4455 + 14 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[3180483,1249780,2143894,2675325,1981932],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[4631220,4633080,4575759,4629108,4638312],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[4631220,4633080,4575759,4629108,4638312],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[3180483,687701,654008,2675325,694154],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[692528,506274,504630,509541,602585],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[3180483,687701,654008,2675325,694154],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[692528,506274,504630,509541,602585],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1,3,2,1,2],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[2,5,4,3,4],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1,3,2,1,2],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[2,5,4,3,4],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675,4639675,4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79","50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4],"assembliesNames":["alg_d1_web_nopac","alg_d1_raw_nopac","alg_d1_frac_nopac","alg_d1_50X_nopac","alg_d1_100X_nopac"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[4631220,1926],[4633080],[4575759,59664,59585,1987,1908],[4629108,1987,1987],[4638312,1760]],"filenames":["alg_d1_web_nopac","alg_d1_raw_nopac","alg_d1_frac_nopac","alg_d1_50X_nopac","alg_d1_100X_nopac"]}
{"lists_of_lengths":[[3180483,692528,605238,128449,1913],[1249780,722451,687701,685668,506274,495955,125667,88600],[2143894,654008,603221,504630,470393,125501,59585,59585,41426,1908,1818,95,74],[2675325,653981,509541,502031,125502,91264,39020,1987,1818,95,74],[1981932,694154,690590,602585,505101,128443,1760]],"filenames":["alg_d1_web_nopac","alg_d1_raw_nopac","alg_d1_frac_nopac","alg_d1_50X_nopac","alg_d1_100X_nopac"]}
{"assemblies_lengths":[4633146,4633080,4698903,4633082,4640072],"filenames":["alg_d1_web_nopac","alg_d1_raw_nopac","alg_d1_frac_nopac","alg_d1_50X_nopac","alg_d1_100X_nopac"]}
{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"alg_d1_frac_nopac":[4396,61,0,3,0],"alg_d1_web_nopac":[4462,3],"alg_d1_50X_nopac":[4448,3,0],"alg_d1_raw_nopac":[4395],"alg_d1_100X_nopac":[4455,0]},"filenames":["alg_d1_web_nopac","alg_d1_raw_nopac","alg_d1_frac_nopac","alg_d1_50X_nopac","alg_d1_100X_nopac"]}
{{ 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.