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":"31 July 2014, Thursday, 13:21:01","report":[["Statistics without reference",[{"values":[4,6,4,4,7,7,3],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[4,6,4,4,7,7,3],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[4,6,4,4,7,7,3],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[1663585,2135901,1671738,1675149,1084537,1812035,1659817],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[2161502,2144412,2160013,2163970,2166318,2157620,2148370],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[2161502,2144412,2160013,2163970,2166318,2157620,2148370],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[2161502,2144412,2160013,2163970,2166318,2157620,2148370],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[1663585,2135901,1671738,1675149,1084537,1812035,1659817],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[1663585,2135901,1671738,1675149,763766,1812035,1659817],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,1,1,1,2,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["39.68","39.53","39.59","39.61","39.58","39.55","39.65"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[2,11,6,5,13,2,3],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[2,9,6,5,13,2,3],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,2,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1,2,2,1,3,1,1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[1663585,2138844,1949937,1675149,2131766,1812035,1659817],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[29,46,33,34,30,37,36],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,4,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,5568,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[46,93,44,68,219,47,37],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[32,48,34,32,57,34,41],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[310,611,269,343,578,299,458],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["2.16","4.43","2.07","3.20","10.34","2.21","1.74"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["1.50","2.29","1.60","1.50","2.69","1.60","1.93"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[22,27,23,22,36,22,27],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[10,21,11,10,21,12,14],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[16423,36771,32523,34824,29330,20243,27242],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["759.80","1714.74","1505.69","1609.26","1353.91","938.21","1268.03"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["98.777","97.199","98.241","98.431","98.033","98.310","98.168"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.013","1.019","1.018","1.017","1.023","1.016","1.013"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["2269 + 17 part","2239 + 33 part","2257 + 18 part","2260 + 27 part","2254 + 22 part","2262 + 19 part","2257 + 22 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[776496,994976,777331,862888,480738,847335,1234602],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[1663585,2135901,1671738,1675149,1084537,1812035,1659817],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[1663585,2135901,1671738,1675149,763766,1812035,1659817],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[468023,459198,467165,467048,257620,828148,1234602],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[403409,175530,397648,364917,117895,828148,483405],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[468023,459198,467165,467048,286777,828148,1234602],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[403409,175530,397648,364917,117895,828148,483405],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,1,1,1,2,1,1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[2,2,2,2,4,2,1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[3,3,3,3,6,2,2],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[2,2,2,2,3,2,1],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[3,3,3,3,6,2,2],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[2160842,2160842,2160842,2160842,2160842,2160842,2160842],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["39.70","39.70","39.70","39.70","39.70","39.70","39.70"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[2301,2301,2301,2301,2301,2301,2301],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3,4,5,6],"assembliesNames":["alg_d3_web_nopac","alg_d3_raw_nopac","alg_d3_frac_nopac","alg_d3_50X_nopac","alg_d3_50X_Jumpall_nopac","alg_d3_100X_nopac","alg_d3_100X_Jumpall_nopac"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[1663585,371176,124098,2643],[2135901,2943,1685,1522,1236,1125],[1671738,278199,207433,2643],[1675149,366232,119726,2863],[1084537,763766,283463,16725,15116,1572,1139],[1812035,318694,10723,10639,2739,1395,1395],[1659817,485690,2863]],"filenames":["alg_d3_web_nopac","alg_d3_raw_nopac","alg_d3_frac_nopac","alg_d3_50X_nopac","alg_d3_50X_Jumpall_nopac","alg_d3_100X_nopac","alg_d3_100X_Jumpall_nopac"]}
{"lists_of_lengths":[[776496,468023,403409,371035,123563,2643],[994976,459198,175530,145855,117928,93507,57632,53975,1792,1151,818,161,93],[777331,467165,397648,206807,157140,116619,2643,1010,818,454],[862888,467048,364917,176704,134661,117606,2863,1633,902],[480738,313246,286777,257620,181703,117895,113538,93649,88250,84332,78954,16725,15116,1937,1748,1572,1139,877,725,114],[847335,828148,316619,118488,10723,10639,2738,1395,1395],[1234602,483405,399053,2863,1010,454]],"filenames":["alg_d3_web_nopac","alg_d3_raw_nopac","alg_d3_frac_nopac","alg_d3_50X_nopac","alg_d3_50X_Jumpall_nopac","alg_d3_100X_nopac","alg_d3_100X_Jumpall_nopac"]}
{"assemblies_lengths":[2161502,2144412,2160013,2163970,2166318,2157620,2148370],"filenames":["alg_d3_web_nopac","alg_d3_raw_nopac","alg_d3_frac_nopac","alg_d3_50X_nopac","alg_d3_50X_Jumpall_nopac","alg_d3_100X_nopac","alg_d3_100X_Jumpall_nopac"]}
{"reflen":2160842}
{"ref_genes_number":2301,"genes_in_contigs":{"alg_d3_frac_nopac":[1718,349,188,2],"alg_d3_50X_Jumpall_nopac":[1106,854,277,15,0,1,1],"alg_d3_100X_Jumpall_nopac":[1703,552,2],"alg_d3_raw_nopac":[2237,2,0,0,0,0],"alg_d3_50X_nopac":[1708,405,146,1],"alg_d3_100X_nopac":[1928,322,9,0,2,1,0],"alg_d3_web_nopac":[1714,406,147,2]},"filenames":["alg_d3_web_nopac","alg_d3_raw_nopac","alg_d3_frac_nopac","alg_d3_50X_nopac","alg_d3_50X_Jumpall_nopac","alg_d3_100X_nopac","alg_d3_100X_Jumpall_nopac"]}
{{ 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.