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, 15:38:09","report":[["Statistics without reference",[{"values":[31,40],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[111,1096],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[25,20],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[1087924,1190496],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4604959,4612084],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4617121,4869716],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4600538,4599141],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[555967,693826],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[360593,652005],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[3,3],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[6,4],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.78","50.73"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[5,3],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[5,2],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,1],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[4,1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[1294499,1190496],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[34,22],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,16],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,13667],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[379,242],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[34,23],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[85,32],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["8.26","5.27"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.74","0.50"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[32,23],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[2,0],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[7456,6273],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["161.91","136.01"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["98.951","98.939"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.004","1.002"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4427 + 25 part","4430 + 21 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[1087682,1088375],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[555967,693826],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[360593,652005],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[368287,651327],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[187109,211555],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[368287,651327],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[187109,211555],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[3,3],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[6,4],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[4,3],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[8,6],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[4,3],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[8,6],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1],"assembliesNames":["spd_d1_web_np","spd_d1_raw_np"]}
{{ qualities }}
{{ mainMetrics }}
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{"assemblies_lengths":[4604959,4612084],"filenames":["spd_d1_web_np","spd_d1_raw_np"]}
{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"spd_d1_raw_np":[1173,1067,674,605,176,203,170,118,113,88,28,4,7,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0],"spd_d1_web_np":[1065,673,560,434,372,331,279,144,140,118,113,89,56,28,3,7,4,4,1,2,0,2,0,1,1,0,0,0,0,0,0]},"filenames":["spd_d1_web_np","spd_d1_raw_np"]}
{{ 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.