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, 16:51:06","report":[["Statistics without reference",[{"values":[40,12,21,12,21,26],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[40,12,21,12,21,26],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[40,12,21,12,21,26],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[532128,1812746,688723,1257198,983533,621920],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4726973,4653487,4656544,4602600,4654299,4508804],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4726973,4653487,4656544,4602600,4654299,4508804],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4726973,4653487,4656544,4602600,4654299,4508804],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[180844,834736,398131,1071366,412226,285200],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[139672,468670,224018,653940,206003,155043],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[9,2,5,2,4,6],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[16,4,9,4,8,11],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.78","50.80","50.77","50.77","50.79","50.86"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[9,9,10,8,15,11],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[8,8,9,7,13,10],"quality":"Less is better","isMain":false,"metricName":" # 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both parts are significant"},{"values":[0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[108,105,117,92,185,282],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[39,35,176,165,133,123],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[78,117,196,179,193,203],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["2.35","2.28","2.53","2.00","4.01","6.26"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.85","0.76","3.81","3.59","2.88","2.73"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[37,34,176,165,131,120],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[2,1,0,0,2,3],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[8,6,1,2,2,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.17","0.13","0.02","0.04","0.04","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.193","99.215","99.620","98.967","99.541","97.023"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.027","1.012","1.008","1.003","1.008","1.002"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4443 + 26 part","4456 + 12 part","4474 + 17 part","4452 + 11 part","4466 + 19 part","4344 + 37 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[532128,1807459,681803,949361,949392,621920],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[182235,834736,398131,1071366,412226,285200],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[143432,468670,224018,653940,206003,140043],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[178261,356726,317322,694380,268132,188512],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[123802,265116,193294,403240,136315,126426],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[178261,356726,317322,694380,268132,188512],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[128407,265116,193294,403240,136315,115335],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[8,2,5,2,4,6],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[15,4,9,4,8,12],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[9,3,5,3,5,7],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[17,6,10,5,11,14],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[9,3,5,3,5,7],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[16,6,10,5,11,15],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[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"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497,4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4,5],"assembliesNames":["4_raw_asm.ctg","4_raw_25X_asm.ctg","4_100X_asm.ctg","4_100X_25X_asm.ctg","4_118X_asm.ctg","4_118X_25X_asm.ctg"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"4_100X_25X_asm.ctg":[1217,1058,679,607,375,105,91,95,89,76,37,23],"4_raw_asm.ctg":[514,473,266,244,213,198,190,177,162,166,183,146,135,144,146,140,129,97,118,68,66,66,57,69,48,32,43,38,29,17,18,8,9,4,7,1,4,3,7,8],"4_118X_asm.ctg":[969,651,456,369,360,270,233,178,191,122,119,99,82,85,71,58,43,40,37,29,4],"4_100X_asm.ctg":[673,649,405,405,385,297,248,211,197,211,168,131,127,112,70,44,46,40,39,16,0],"4_raw_25X_asm.ctg":[1736,806,457,470,344,212,120,104,62,71,43,31],"4_118X_25X_asm.ctg":[572,490,326,361,277,269,206,198,212,175,162,141,130,124,114,105,88,89,56,42,34,40,37,29,37,30]},"filenames":["4_raw_asm.ctg","4_raw_25X_asm.ctg","4_100X_asm.ctg","4_100X_25X_asm.ctg","4_118X_asm.ctg","4_118X_25X_asm.ctg"]}
{{ operonsInContigs }}
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tg","4_118X_asm.ctg","4_118X_25X_asm.ctg"]}
{
"# 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.