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":"30 July 2013, Tuesday, 10:32:56","report":[["Basic statistics",[{"values":[74,33,61,341,56,53,78,32],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[74,33,61,341,56,53,78,32],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[71,33,48,310,51,38,70,27],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[430487,1198056,1197734,106317,1194879,1202947,896381,1205706],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[5380708,5420940,5433046,5321914,5344353,5379795,5356258,5469099],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[5380708,5420940,5433046,5321914,5344353,5379795,5356258,5469099],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[5378420,5420940,5423253,5300702,5341261,5371096,5351096,5465903],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[5432652,5432652,5432652,5432652,5432652,5432652,5432652,5432652],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":[135613,431479,337861,25876,456635,485493,247748,487570],"quality":"More is better","isMain":false,"metricName":"N50"},{"values":[74995,211009,209762,16762,128609,208962,88406,257548],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[135613,431479,337861,25512,456635,485493,247748,487570],"quality":"More is better","isMain":true,"metricName":"NG50"},{"values":[74197,211009,209762,15678,116644,181669,88406,257548],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[11,4,4,63,4,3,6,3],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[24,9,10,126,10,8,14,8],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":[11,4,4,65,4,3,6,3],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[25,9,10,132,11,9,14,8],"quality":"Less is better","isMain":false,"metricName":"LG75"}]],["Misassemblies",[{"values":[4,15,15,3,1,3,9,11],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[3,12,13,3,1,3,9,8],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[1,3,2,0,0,0,0,3],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[4,9,13,3,1,3,5,9],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[155883,1987058,765654,24763,90965,94799,723259,2399227],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[30,12,13,1,41,9,263,8],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0,1,12,1,5],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,2316,6892,2330,3196],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0,0,1,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0,0,74,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Genome statistics",[{"values":["98.444","99.334","99.009","97.438","98.099","98.554","97.523","99.380"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.010","1.018","1.011","1.004","1.029","1.005","1.010","1.017"],"quality":"Less is better","isMain":false,"metricName":"Duplication ratio"},{"values":["5819 + 64 part","5965 + 34 part","5964 + 34 part","5635 + 231 part","5839 + 44 part","5950 + 27 part","5604 + 275 part","5980 + 28 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":["35.30","35.41","35.39","35.27","35.29","35.35","35.30","35.41"],"quality":"Equal","isMain":false,"metricName":"GC (%)"},{"values":["35.50","35.50","35.50","35.50","35.50","35.50","35.50","35.50"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":["6.62","4.43","8.96","0.70","8.16","2.07","5.93","6.08"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":[354,239,482,37,435,111,314,328],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":["7.57","5.86","5.95","2.00","5.69","2.39","30.28","2.78"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[405,316,320,106,303,128,1604,150],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[310,286,316,100,285,120,1577,141],"quality":"Less is better","isMain":false,"metricName":" # short indels (<= 5 bp)"},{"values":[95,30,4,6,18,8,27,9],"quality":"Less is better","isMain":false,"metricName":" # long indels (> 5 bp)"},{"values":[2870,895,461,277,707,333,2559,353],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":[6265,945,407,0,455,820,41988,2],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["116.43","17.43","7.49","0.00","8.51","15.24","783.91","0.04"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Aligned statistics",[{"values":[430487,1197973,1197581,106317,1194643,1202947,890081,1205705],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[135296,288228,337861,25876,455989,485493,208398,487570],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[74995,131868,184731,16315,128609,208962,87283,211605],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[135296,288228,337861,25512,455989,485493,208398,487570],"quality":"More is better","isMain":false,"metricName":"NGA50"},{"values":[73848,131868,184731,15663,116644,181669,80463,211605],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[11,5,4,63,4,3,7,3],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[24,11,10,127,10,8,15,8],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[11,5,4,65,4,3,7,3],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[25,11,10,132,11,9,16,8],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]]],"minContig":500,"assembliesNames":["abyss_scf","cabog_scf","msrca_scf","sga_scf","soap_scf","spades2.5_scf","velvet_scf","CISA_result"]}
{{ qualities }}
{{ mainMetrics }}
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{"assemblies_lengths":[5380708,5420940,5433046,5321914,5344353,5379795,5356258,5469099],"filenames":["abyss_scf","cabog_scf","msrca_scf","sga_scf","soap_scf","spades2.5_scf","velvet_scf","CISA_result"]}
{"reflen":5432652}
{"ref_genes_number":6014,"genes_in_contigs":{"soap_scf":[1324,782,520,505,274,244,217,198,207,129,131,109,129,93,90,72,72,82,85,74,53,48,45,45,43,24,38,27,17,18,27,25,18,19,8,7,9,7,5,3,2,3,0,0,0,0,0,0,6,0,2,0,3,0,0,0],"msrca_scf":[1329,857,524,384,277,240,237,219,247,213,218,207,160,121,122,94,76,55,51,46,52,25,30,18,27,24,15,24,20,11,4,5,6,1,1,0,14,0,0,0,0,0,1,0,0,0,0,4,0,0,0,0,0,0,5,0,0,0,0,0,0],"CISA_result":[1364,1331,524,355,327,277,310,217,213,207,162,146,121,94,72,76,55,44,17,24,20,11,5,6,0,2,0,0,0,0,0,0],"velvet_scf":[966,755,421,370,266,250,212,220,213,154,151,124,120,90,69,82,66,64,62,71,66,60,64,49,48,52,52,33,25,33,32,28,28,28,25,20,15,20,17,10,21,9,14,11,14,12,8,9,5,7,12,6,8,5,5,3,1,5,0,1,0,3,0,0,0,0,0,0,0,0,2,6,0,6,0,0,0,0],"abyss_scf":[464,467,319,317,274,269,219,208,146,130,150,132,148,134,131,118,110,120,117,112,95,84,91,72,94,62,59,70,75,73,57,52,50,55,53,54,48,46,40,47,34,40,23,30,35,29,27,25,25,15,19,11,17,15,20,18,16,10,7,4,9,9,5,4,2,0,0,4,0,4,0,0,0,0],"cabog_scf":[1330,832,463,493,328,276,313,264,213,207,145,133,131,120,94,90,72,57,76,61,55,44,30,28,17,24,20,15,12,11,5,6,0],"sga_scf":[105,96,93,97,58,62,54,64,62,63,67,56,46,60,56,50,52,52,48,44,53,48,47,40,47,44,57,39,45,41,43,47,39,44,41,44,35,40,45,35,31,50,34,41,44,40,29,34,36,28,33,41,37,33,40,26,43,27,34,29,27,32,32,28,25,18,29,24,32,26,24,24,24,23,30,29,30,24,25,22,25,16,20,20,22,18,16,22,21,30,20,21,18,19,18,15,15,20,27,22,21,20,21,17,26,22,18,25,19,22,14,25,15,19,22,21,17,15,21,16,13,19,16,22,14,16,19,17,17,17,13,14,13,16,19,15,15,17,15,15,13,16,14,11,15,11,16,16,14,13,14,9,11,17,12,12,14,19,13,10,11,9,14,12,12,7,16,13,14,11,8,16,10,13,12,14,8,10,11,12,4,8,10,8,8,9,11,8,12,8,4,11,6,7,12,9,14,7,9,6,7,8,7,7,8,8,6,0,10,7,9,7,5,5,7,8,5,2,4,8,0,9,9,6,4,5,8,7,6,8,5,5,5,4,6,5,5,7,6,4,5,4,8,4,3,6,6,4,5,4,3,3,3,5,4,3,4,5,3,3,4,2,3,4,2,2,2,2,2,5,4,3,1,3,2,3,2,3,3,0,2,4,3,1,1,2,2,2,1,0,3,1,1,2,4,0,2,1,0,2,0,0,2,1,1,0,0,2,1,0,0,0,0,0,0,0,8,0,0,0,0,0,0,5,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,3,0],"spades2.5_scf":[1360,1329,523,327,277,245,217,213,191,207,145,130,121,94,90,72,72,76,55,49,43,28,17,20,20,11,7,5,0,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]},"filenames":["abyss_scf","cabog_scf","msrca_scf","sga_scf","soap_scf","spades2.5_scf","velvet_scf","CISA_result"]}
{{ 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 minimum 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 minimum 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.