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":"28 December 2014, Sunday, 16:39:14","report":[["Statistics without reference",[{"values":[1,5,1,6,1,1,1,1,1,1],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[1,5,1,6,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[1,5,1,6,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[4648864,3621580,4639780,2212593,4651575,4645728,4647827,4649239,4648687,4648099],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4648864,4636448,4639780,4650421,4651575,4645728,4647827,4649239,4648687,4648099],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4648864,4636448,4639780,4650421,4651575,4645728,4647827,4649239,4648687,4648099],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4648864,4636448,4639780,4650421,4651575,4645728,4647827,4649239,4648687,4648099],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[4648864,3621580,4639780,887256,4651575,4645728,4647827,4649239,4648687,4648099],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[4648864,3621580,4639780,757877,4651575,4645728,4647827,4649239,4648687,4648099],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,2,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,1,1,3,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.78","50.81","50.80","50.79","50.78","50.79","50.78","50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[10,8,8,8,8,8,10,9,8,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[8,7,7,7,7,7,8,8,7,7],"quality":"Less is better","isMain":false,"metricName":" # 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short indels"},{"values":[2,14,8,1,3,2,0,3,3,0],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.00","0.00","0.00","0.00","0.00","0.00","0.00","0.00","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["100.000","99.900","99.965","99.981","100.000","100.000","100.000","100.000","100.000","100.000"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.002","1.000","1.000","1.003","1.003","1.001","1.002","1.002","1.002","1.002"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4494 + 3 part","4486 + 8 part","4491 + 5 part","4491 + 6 part","4494 + 3 part","4494 + 3 part","4494 + 3 part","4494 + 3 part","4494 + 3 part","4494 + 3 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[3026386,1098943,1926349,1554363,3026238,2603928,3026270,1773437,2856673,2856687],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[4648864,3621580,4639780,887256,4651575,4645728,4647827,4649239,4648687,4648099],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[4648864,3621580,4639780,757877,4651575,4645728,4647827,4649239,4648687,4648099],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[3026386,907076,1097763,880448,3026238,2603928,3026270,1257068,2856673,2856687],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[949273,770984,949088,572235,949262,949201,949234,949269,949217,949251],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[3026386,907076,1097763,880448,3026238,2603928,3026270,1257068,2856673,2856687],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[949273,770984,949088,572235,949262,949201,949234,949269,949217,949251],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,1,2,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,1,1,3,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1,3,2,2,1,1,1,2,1,1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[2,4,3,4,2,2,2,3,2,2],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1,3,2,2,1,1,1,2,1,1],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[2,4,3,4,2,2,2,3,2,2],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4639675,4639675,4639675,4639675,4639675,4639675,4639675,4639675,4639675,4639675],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["50.79","50.79","50.79","50.79","50.79","50.79","50.79","50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4497,4497,4497,4497,4497,4497,4497,4497,4497,4497],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4,5,6,7,8,9],"assembliesNames":["f25_d5_all","f25_d5_rg4_1","f25_d5_rg4_2","f25_d5_rg4_3","f25_d5_rg6_1","f25_d5_rg6_2","f25_d5_rg6_3","f25_d5_rg8_1","f25_d5_rg8_2","f25_d5_rg8_3"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[4648864],[3621580,770984,162243,47782,33859],[4639780],[2212593,887256,757877,400005,213477,179213],[4651575],[4645728],[4647827],[4649239],[4648687],[4648099]],"filenames":["f25_d5_all","f25_d5_rg4_1","f25_d5_rg4_2","f25_d5_rg4_3","f25_d5_rg6_1","f25_d5_rg6_2","f25_d5_rg6_3","f25_d5_rg8_1","f25_d5_rg8_2","f25_d5_rg8_3"]}
{"lists_of_lengths":[[3026386,949273,572335,89891,4022,1818,1817,1199,769,768,586],[1098943,949008,907076,770984,572135,162243,89866,47782,33859,1817,1198,769,768],[1926349,1097763,949088,572167,89857,1818,1201,769,768],[1554363,880448,688399,572235,400005,213477,179213,84022,68710,4990,1818,1204,769,768],[3026238,949262,328446,253205,89868,1818,1201,769,768],[2603928,949201,572265,425915,89864,1817,1201,769,768],[3026270,949234,572305,89886,3301,1818,1817,1199,769,768,460],[1773437,1257068,949269,572308,89889,2714,1818,1199,769,768],[2856673,949217,572305,176054,89882,1818,1201,769,768],[2856687,949251,572307,175435,89863,1818,1201,769,768]],"filenames":["f25_d5_all","f25_d5_rg4_1","f25_d5_rg4_2","f25_d5_rg4_3","f25_d5_rg6_1","f25_d5_rg6_2","f25_d5_rg6_3","f25_d5_rg8_1","f25_d5_rg8_2","f25_d5_rg8_3"]}
{"assemblies_lengths":[4648864,4636448,4639780,4650421,4651575,4645728,4647827,4649239,4648687,4648099],"filenames":["f25_d5_all","f25_d5_rg4_1","f25_d5_rg4_2","f25_d5_rg4_3","f25_d5_rg6_1","f25_d5_rg6_2","f25_d5_rg6_3","f25_d5_rg8_1","f25_d5_rg8_2","f25_d5_rg8_3"]}
{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"f25_d5_rg6_3":[4494],"f25_d5_all":[4494],"f25_d5_rg4_2":[4491],"f25_d5_rg4_3":[2160,852,731,387,203,158],"f25_d5_rg4_1":[3507,750,150,51,28],"f25_d5_rg6_1":[4494],"f25_d5_rg8_2":[4494],"f25_d5_rg8_3":[4494],"f25_d5_rg6_2":[4494],"f25_d5_rg8_1":[4494]},"filenames":["f25_d5_all","f25_d5_rg4_1","f25_d5_rg4_2","f25_d5_rg4_3","f25_d5_rg6_1","f25_d5_rg6_2","f25_d5_rg6_3","f25_d5_rg8_1","f25_d5_rg8_2","f25_d5_rg8_3"]}
{{ 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.