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, 13:50:43","report":[["Statistics without reference",[{"values":[11,13,10,12],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[11,13,11,12],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[11,13,10,12],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[3188818,3188540,3188847,3188773],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4601792,4588701,4609235,4602493],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4601792,4588701,4609705,4602493],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4601792,4588701,4609235,4602493],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[3188818,3188540,3188847,3188773],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[942937,942929,942929,943582],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[2,2,2,2],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["68.79","68.80","68.79","68.80"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[3,3,4,4],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[0,1,0,1],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[3,2,4,3],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[2,2,3,3],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[133056,1067239,206335,196336],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[7,6,8,11],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[140,169,191,292],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[134,180,168,252],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[293,316,266,386],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["3.04","3.69","4.15","6.35"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["2.91","3.93","3.65","5.48"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[125,172,161,244],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[9,8,7,8],"quality":"Less is better","isMain":false,"metricName":" # long indels"},{"values":[0,4,6,2073],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.09","0.13","45.04"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Genome statistics",[{"values":["99.921","99.583","99.927","99.834"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.001","1.001","1.002","1.002"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4381 + 6 part","4365 + 11 part","4379 + 7 part","4372 + 14 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[3188814,3188540,3188795,3188333],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[3188818,3188540,3188847,3188773],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[942937,942929,942929,943582],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[3188814,3188540,3188795,3188333],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[942936,938038,942927,943580],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[3188814,3188540,3188795,3188333],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[942936,938038,942927,943580],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[2,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[2,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LGA50"},{"values":[2,2,2,2],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Predicted genes",[]],["Reference statistics",[{"values":[4603060,4603060,4603060,4603060],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":["68.79","68.79","68.79","68.79"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[4388,4388,4388,4388],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"minContig":500,"order":[0,1,2,3],"assembliesNames":["alg_d2_web","alg_d2_raw","alg_d2_frac","alg_d2_100X"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[3188818,942937,124310,114178,105281,65387,19264,15458,9991,8746,7422],[3188540,942929,124310,114178,105281,62893,15522,10112,8809,6935,4325,2672,2195],[3188847,942929,124310,114178,105281,73279,19264,17413,14988,8746],[3188773,943582,124310,114178,105281,63280,19264,15458,9991,8746,7422,2208]],"filenames":["alg_d2_web","alg_d2_raw","alg_d2_frac","alg_d2_100X"]}
{"lists_of_lengths":[[3188814,942936,113578,105281,87228,65387,30460,19264,15451,9991,7422,7111,6622,1635],[3188540,938038,113834,105281,66391,62893,37087,20831,15522,10112,8808,6900,4890,4325,2672,2195],[3188795,942927,114177,105281,87228,65595,34958,19264,17413,14988,7684,7111,2124,1635],[3188333,943580,114178,105281,87228,39651,30354,21911,19264,15451,9991,7422,7111,6728,2208,1635]],"filenames":["alg_d2_web","alg_d2_raw","alg_d2_frac","alg_d2_100X"]}
{"assemblies_lengths":[4601792,4588701,4609235,4602493],"filenames":["alg_d2_web","alg_d2_raw","alg_d2_frac","alg_d2_100X"]}
{"reflen":4603060}
{"ref_genes_number":4388,"genes_in_contigs":{"alg_d2_web":[3104,872,103,102,90,67,18,12,3,7,3],"alg_d2_raw":[3104,868,102,102,90,66,10,8,3,6,4,0,2],"alg_d2_100X":[3101,870,103,101,89,64,18,12,3,7,3,1],"alg_d2_frac":[3103,871,103,101,90,72,18,3,11,7]},"filenames":["alg_d2_web","alg_d2_raw","alg_d2_frac","alg_d2_100X"]}
{{ 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.