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, 16:12:46","report":[["Statistics without reference",[{"values":[86,15,14,12,11,6,6],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[546,451,442,438,437,432,432],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[73,11,10,8,7,2,2],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[285889,2498709,3196491,1522255,2216997,4644452,4644455],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4577132,4626443,4639784,4651072,4649795,4652420,4652423],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4696376,4738846,4750609,4761640,4760363,4762988,4762991],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4567893,4623938,4637279,4648567,4647290,4649915,4649918],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[139882,2498709,3196491,1241619,1750947,4644452,4644455],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[78649,654474,657335,979451,1750947,4644452,4644455],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[11,1,1,2,2,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[22,3,2,3,2,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.74","50.78","50.78","50.78","50.78","50.78","50.78"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[2,6,6,7,7,7,7],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[2,6,6,7,7,7,7],"quality":"Less is better","isMain":false,"metricName":" # 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{{ qualities }}
{{ mainMetrics }}
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{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"spd_hb_4cell":[2167,1666,454,201,0,4,0,0,0,0,0],"spd_hb_3cell":[1487,1150,963,885,0,2,3,2,0,0,0,0],"spd_hb_2cell":[3131,610,290,203,157,89,2,0,1,2,0,0,0,0],"spd_hb_p4c2":[4495,0,0,0,0,0],"spd_miseq":[270,240,265,206,212,191,221,175,171,141,120,122,119,113,101,102,112,95,83,89,96,73,60,57,57,51,54,54,56,44,37,60,42,42,31,38,41,29,38,28,37,19,25,27,30,14,18,11,7,8,13,9,0,7,7,4,2,5,1,2,2,3,2,1,2,1,2,1,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0],"spd_hb_1cell":[2450,678,609,325,173,117,89,37,0,0,1,0,0,0,0],"spd_hb_17cell":[4495,0,0,0,0,0]},"filenames":["spd_miseq","spd_hb_1cell","spd_hb_2cell","spd_hb_3cell","spd_hb_4cell","spd_hb_17cell","spd_hb_p4c2"]}
{{ 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.