Loading...
{"date":"21 May 2021, Friday, 20:22:52","assembliesNames":["CV45_spades_contigs"],"referenceName":"NC_045512.2","order":[0],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["94.957"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.011"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["31 + 22 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[6779],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[28602],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[2447],"isMain":false},{"metricName":"NG75","quality":"More is better","values":[1473],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[1043],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[2447],"isMain":true},{"metricName":"NGA75","quality":"More is better","values":[1473],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[4],"isMain":false},{"metricName":"LG75","quality":"Less is better","values":[8],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[12],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[4],"isMain":true},{"metricName":"LGA75","quality":"Less is better","values":[8],"isMain":false}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0],"isMain":false},{"metricName":"# scaffold gap ext. mis.","quality":"Less is better","values":[0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0],"isMain":false},{"metricName":"# unaligned mis. contigs","quality":"Less is better","values":[0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[32],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[25934],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches","quality":"Less is better","values":[35],"isMain":false},{"metricName":"# indels","quality":"Less is better","values":[12],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[51],"isMain":false},{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["123.26"],"isMain":true},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["42.26"],"isMain":true},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[10],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[2],"isMain":false},{"metricName":"# N's","quality":"Less is better","values":[0],"isMain":false},{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[45],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[518],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[18],"isMain":false},{"metricName":"# contigs (>= 5000 bp)","quality":"Equal","values":[1],"isMain":false},{"metricName":"# contigs (>= 10000 bp)","quality":"Equal","values":[0],"isMain":false},{"metricName":"# contigs (>= 25000 bp)","quality":"Equal","values":[0],"isMain":false},{"metricName":"# contigs (>= 50000 bp)","quality":"Equal","values":[0],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[6779],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[54635],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[117647],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[35290],"isMain":true},{"metricName":"Total length (>= 5000 bp)","quality":"More is better","values":[6779],"isMain":false},{"metricName":"Total length (>= 10000 bp)","quality":"More is better","values":[0],"isMain":true},{"metricName":"Total length (>= 25000 bp)","quality":"More is better","values":[0],"isMain":false},{"metricName":"Total length (>= 50000 bp)","quality":"More is better","values":[0],"isMain":true},{"metricName":"N50","quality":"More is better","values":[1255],"isMain":false},{"metricName":"N75","quality":"More is better","values":[869],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[11],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[25],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["44.03"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[{"metricName":"# similar correct contigs","quality":"Equal","values":[0],"isMain":false},{"metricName":"# similar misassembled blocks","quality":"Equal","values":[0],"isMain":false}]],["Reference statistics",[{"metricName":"Reference length","quality":"Equal","values":[29903],"isMain":false},{"metricName":"Reference fragments","quality":"Equal","values":[1],"isMain":false},{"metricName":"Reference GC (%)","quality":"Equal","values":["37.97"],"isMain":false},{"metricName":"Reference genomic features","quality":"Equal","values":[59],"isMain":false}]]],"subreferences":[],"subreports":[],"minContig":500}
{{ qualities }}
{{ mainMetrics }}
{"filenames":["CV45_spades_contigs"],"lists_of_lengths":[[6779,3887,3706,2447,1768,1689,1494,1473,1457,1372,1255,1252,1242,1145,1133,1081,1067,1043,983,959,940,907,906,897,869,813,766,745,743,739,705,672,647,636,636,633,621,621,608,606,590,539,531,529,504]]}
{"filenames":["CV45_spades_contigs"],"assemblies_lengths":[54635]}
{"reflen":[29903]}
{"tickX":1}
{"coord_x":[[0.0,1e-10,12.407797199597328,12.407797199697328,19.522284250022878,19.522284250122876,26.3054818339892,26.3054818340892,30.784295781092705,30.784295781192704,34.020316646838104,34.020316646938106,37.11174155760959,37.11174155770959,39.84625240230621,39.846252402406215,42.54232634757939,42.54232634767939,45.20911503614899,45.20911503624899,47.72032579848083,47.72032579858083,50.01738812116775,50.01738812126775,52.30895945822275,52.308959458322754,54.58222750983801,54.582227509938015,56.67795369268784,56.67795369278784,58.751715933009976,58.75171593310998,60.73030108904548,60.730301089145485,62.68326164546536,62.68326164556536,64.59229431682986,64.59229431692987,66.39150727555597,66.39150727565597,68.14679234922669,68.14679234932669,69.86730118056191,69.86730118066191,71.52740916994601,71.52740917004601,73.18568683078612,73.18568683088613,74.82749153473048,74.82749153483049,76.41804703944358,76.41804703954358,77.90610414569416,77.90610414579416,79.30813581037796,79.30813581047796,80.67173057563832,80.67173057573832,82.03166468381075,82.03166468391075,83.38427747780726,83.38427747790726,84.67465910130869,84.6746591014087,85.90463988285897,85.90463988295897,87.08886245080993,87.08886245090993,88.25295140477716,88.25295140487717,90.57563832707972,90.57563832717972,91.71227235288734,91.71227235298734,93.96174613343095,93.96174613353095,95.07092523107897,95.07092523117898,96.15081907202342,96.15081907212343,97.13736615722522,97.13736615732522,98.10927061407523,98.10927061417523,99.07751441383728,99.07751441393728,100.0]],"coord_y":[[6779,6779,6779,3887,3887,3706,3706,2447,2447,1768,1768,1689,1689,1494,1494,1473,1473,1457,1457,1372,1372,1255,1255,1252,1252,1242,1242,1145,1145,1133,1133,1081,1081,1067,1067,1043,1043,983,983,959,959,940,940,907,907,906,906,897,897,869,869,813,813,766,766,745,745,743,743,739,739,705,705,672,672,647,647,636,636,633,633,621,621,608,608,606,606,590,590,539,539,531,531,529,529,504,504]],"filenames":["CV45_spades_contigs"]}
{"coord_x":[[0.0,1e-10,22.66996622412467,22.66996622422467,35.66866200715647,35.66866200725647,48.062067351101895,48.0620673512019,56.245192790021065,56.24519279012107,62.15764304584824,62.15764304594824,67.80590576196369,67.80590576206369,72.80205999398054,72.80205999408054,77.72798715847908,77.72798715857908,82.60040798582082,82.60040798592082,87.18857639701702,87.18857639711702,91.38547971775407,91.38547971785407,95.57235060027422,95.57235060037422,99.72578002207136,99.72578002217136,103.55482727485537,103.55482727495537,107.34374477477176,107.34374477487177,110.95876667892854,110.95876667902854,114.5269705380731,114.5269705381731,118.01491489148246,118.01491489158246,121.3022104805538,121.3022104806538,124.50924656388992,124.50924656398992,127.65274387185232,127.65274387195232,130.68588435942883,130.6858843595288,133.715680700933,133.715680701033,136.7153797277865,136.7153797278865,139.62144266461559,139.62144266471557,142.34023342139585,142.34023342149584,144.90184931277798,144.90184931287797,147.3932381366418,147.3932381367418,149.87793866836103,149.877938668461,152.34926261579105,152.34926261589104,154.70688559676287,154.70688559686286,156.95415175734877,156.95415175744876,159.11781426612714,159.11781426622713,161.24469116811022,161.2446911682102,165.48841253385947,165.48841253395946,167.56512724475806,167.56512724485805,171.6750827676153,171.67508276771528,173.70163528742935,173.70163528752934,175.67468147008663,175.6746814701866,177.47717620305656,177.47717620315655,179.25291776744808,179.25291776754807,181.02197103969502,181.021971039795,182.70742066013443]],"coord_y":[[6779,6779,6779,3887,3887,3706,3706,2447,2447,1768,1768,1689,1689,1494,1494,1473,1473,1457,1457,1372,1372,1255,1255,1252,1252,1242,1242,1145,1145,1133,1133,1081,1081,1067,1067,1043,1043,983,983,959,959,940,940,907,907,906,906,897,897,869,869,813,813,766,766,745,745,743,743,739,739,705,705,672,672,647,647,636,636,633,633,621,621,608,608,606,606,590,590,539,539,531,531,529,529,504,504]],"filenames":["CV45_spades_contigs"]}
{"coord_x":[[0.0,1e-10,12.407797199597328,12.407797199697328,19.522284250022878,19.522284250122876,26.3054818339892,26.3054818340892,30.784295781092705,30.784295781192704,34.020316646838104,34.020316646938106,37.02571611604283,37.02571611614283,39.76022696073945,39.760226960839454,42.45630090601263,42.45630090611263,45.123089594582225,45.12308959468223,47.32497483298252,47.32497483308252,49.2779353894024,49.2779353895024,51.18696806076691,51.18696806086691,52.351057014734145]],"coord_y":[[6779,6779,6779,3887,3887,3706,3706,2447,2447,1768,1768,1642,1642,1494,1494,1473,1473,1457,1457,1203,1203,1067,1067,1043,1043,636,636]],"filenames":["CV45_spades_contigs"]}
{"coord_x":[[0.0,1e-10,22.66996622412467,22.66996622422467,35.66866200715647,35.66866200725647,48.062067351101895,48.0620673512019,56.245192790021065,56.24519279012107,62.15764304584824,62.15764304594824,67.64873089656557,67.64873089666557,72.64488512858242,72.64488512868242,77.57081229308096,77.57081229318096,82.4432331204227,82.4432331205227,86.46624084540012,86.46624084550012,90.0344447045447,90.0344447046447,93.52238905795406,93.52238905805406,95.64926595993713]],"coord_y":[[6779,6779,6779,3887,3887,3706,3706,2447,2447,1768,1768,1642,1642,1494,1494,1473,1473,1457,1457,1203,1203,1067,1067,1043,1043,636,636]],"filenames":["CV45_spades_contigs"]}
{"coord_x":[[0,1]],"coord_y":[[95.64926595993713,95.64926595993713]],"filenames":["CV45_spades_contigs"]}
{"filenames":["CV45_spades_contigs"],"features_in_contigs":{"CV45_spades_contigs":[10,0,6,12,0,0,0,0,1,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]},"ref_features_number":59}
{{ operonsInContigs }}
[{{ num_contigs }},
{{ Largest_alignment }},
{{ Total_aligned_length }},
{{ num_misassemblies }},
{{ Misassembled_contigs_length }},
{{ num_mismatches_per_100_kbp }},
{{ num_indels_per_100_kbp }},
{{ num_N's_per_100_kbp }},
{{ Genome_fraction }},
{{ Duplication_ratio }},
{{ NGA50 }}]
{{ allMisassemblies }}
{{ krona }}
{"filenames":["CV45_spades_contigs"],"reference_index":1,"list_of_GC_distributions":[[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,1,5,5,8,19,12,17,21,27,18,39,24,14,15,24,16,17,13,20,28,19,18,20,28,21,17,19,19,10,10,6,3,4,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,2,1,1,0,4,6,11,15,16,20,25,22,26,19,26,17,19,15,12,6,11,6,5,1,4,1,0,4,2,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"list_of_GC_contigs_distributions":[[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,1,10,0,17,16,1,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null}
{"links":["icarus_viewers/alignment_viewer.html"],"links_names":["View in Icarus contig browser"]}
{
"# 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.",
"# contigs (>= 0 bp)" : "is the total number of contigs in the assembly that have size greater than or equal to 0 bp.",
"Total length (>= 0 bp)" : "is the total number of bases in the contigs having size greater than or equal to 0 bp.",
"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).",
"# large block misassemblies" : "is the number of misassemblies between alignments with length greater than or equal to 3 kbp and with the misassembly threshold equal to 5 kbp (instead of default 1 kbp for regular misassemblies).",
"# 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.",
"# interspecies translocations" : "is the number of interspecies translocation events among all misassembly events. Interspecies translocation is a misassembly where the flanking sequences align on different references (based on alignments to the combined reference).",
"# 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.",
"# large relocations" : "is the number of relocation events among all large block misassemblies. Relocation is a misassembly where the left flanking sequence aligns over 5 kbp away from the right flanking sequence on the reference, or they overlap by more than 5 kbp and both flanking sequences align on the same chromosome.",
"# large translocations" : "is the number of translocation events among all large block misassemblies. Translocation is a misassembly where the flanking sequences align on different chromosomes.",
"# large i/s translocations" : "is the number of interspecies translocation events among all large block misassemblies. Interspecies translocation is a misassembly where the flanking sequences align on different references (based on alignments to the combined reference).",
"# large inversions" : "is the number of inversion events among all large block misassemblies. 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 the misassembly threshold (1 kbp by default).
- The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.
- There are two misassembly breakpoints of the same type around a short alignment (less than 7 kbp by default)
- The gap between two long flanking sequences on the sides of the short alignment is less than 7 kbp.
- The long flanking sequences both are on the same strand of the same chromosome of the reference genome.