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, 14:48:31","report":[["Statistics without reference",[{"values":[1,4,1,6,1,1,1,1,1,1],"quality":"Less is better","isMain":true,"metricName":"# contigs"},{"values":[1,4,1,6,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[1,4,1,6,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[4649001,3622531,4647261,3760960,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[4649001,4638443,4647261,4661578,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[4649001,4638443,4647261,4661578,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[4649001,4638443,4647261,4661578,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"More is better","isMain":false,"metricName":"Total length (>= 1000 bp)"},{"values":[4649001,3622531,4647261,3760960,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"More is better","isMain":true,"metricName":"N50"},{"values":[4649001,3622531,4647261,3760960,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,1,1,1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["50.78","50.80","50.79","50.79","50.79","50.78","50.78","50.79","50.79","50.79"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Misassemblies",[{"values":[10,8,8,10,8,8,10,9,8,8],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[8,7,7,9,7,7,8,8,7,7],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[2,1,1,1,1,1,2,1,1,1],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1,1,1,2,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[4649001,3622531,4647261,3864655,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[2,2,2,2,2,2,2,2,3,2],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"}]],["Unaligned",[{"values":[0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # with misassembly"},{"values":[0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # both parts are significant"},{"values":[0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[9,23,12,45,10,13,12,12,4,6],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[76,1225,935,736,309,499,270,190,246,310],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[97,1386,1051,773,322,523,278,223,261,327],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.19","0.50","0.26","0.97","0.22","0.28","0.26","0.26","0.09","0.13"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["1.64","26.42","20.15","15.86","6.66","10.76","5.82","4.10","5.30","6.68"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[74,1216,928,734,309,497,270,188,246,310],"quality":"Less is better","isMain":false,"metricName":" # short indels"},{"values":[2,9,7,2,0,2,0,2,0,0],"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","99.942","100.000","99.999","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","1.002","1.006","1.002","1.003","1.002","1.002","1.002","1.002"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["4494 + 3 part","4488 + 8 part","4494 + 3 part","4492 + 5 part","4494 + 3 part","4495 + 2 part","4494 + 3 part","4494 + 3 part","4494 + 3 part","4494 + 3 part"],"quality":"More is better","isMain":true,"metricName":"# genes"},{"values":[3026385,1099780,2172678,1555737,3026217,3026142,3026271,1773451,2856677,2856668],"quality":"More is better","isMain":false,"metricName":"Largest alignment"},{"values":[4649001,3622531,4647261,3760960,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[4649001,3622531,4647261,3760960,4648404,4654462,4647823,4649251,4648711,4648069],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[3026385,907188,949093,880427,3026217,3026142,3026271,1257063,2856677,2856668],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[949275,771221,858856,572240,949225,955929,949237,949274,949249,949243],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[3026385,907188,949093,880427,3026217,3026142,3026271,1257063,2856677,2856668],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[949275,771221,858856,572240,949225,955929,949237,949274,949249,949243],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,1,1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,1,1,1,1,1,1,1,1,1],"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":["f25X_d5_all_wog","f25X_d5_rg4_1_wog","f25X_d5_rg4_2_wog","f25X_d5_rg4_3_wog","f25X_d5_rg6_1_wog","f25X_d5_rg6_2_wog","f25X_d5_rg6_3_wog","f25X_d5_rg8_1_wog","f25X_d5_rg8_2_wog","f25X_d5_rg8_3_wog"]}
{{ qualities }}
{{ mainMetrics }}
{"lists_of_lengths":[[4649001],[3622531,771221,210441,34250],[4647261],[3760960,400160,229868,121911,103695,44984],[4648404],[4654462],[4647823],[4649251],[4648711],[4648069]],"filenames":["f25X_d5_all_wog","f25X_d5_rg4_1_wog","f25X_d5_rg4_2_wog","f25X_d5_rg4_3_wog","f25X_d5_rg6_1_wog","f25X_d5_rg6_2_wog","f25X_d5_rg6_3_wog","f25X_d5_rg8_1_wog","f25X_d5_rg8_2_wog","f25X_d5_rg8_3_wog"]}
{"lists_of_lengths":[[3026385,949275,572333,89891,4160,1818,1817,1199,769,768,586],[1099780,948999,907188,771221,572167,210441,89842,34250,1818,1201,768,768],[2172678,949093,858856,572220,89858,1818,1201,769,768],[1555737,880427,656986,572240,400160,229868,121911,89852,68709,44984,34217,1931,1818,1201,769,768],[3026217,949225,408621,169902,89885,1818,1199,769,768],[3026142,955929,572251,89864,5720,1818,1201,769,768],[3026271,949237,572299,89885,3301,1818,1816,1199,769,768,460],[1773451,1257063,949274,572307,89889,2713,1818,1199,769,768],[2856677,949249,572304,176054,89871,1818,1201,769,768],[2856668,949243,572305,175433,89864,1818,1201,769,768]],"filenames":["f25X_d5_all_wog","f25X_d5_rg4_1_wog","f25X_d5_rg4_2_wog","f25X_d5_rg4_3_wog","f25X_d5_rg6_1_wog","f25X_d5_rg6_2_wog","f25X_d5_rg6_3_wog","f25X_d5_rg8_1_wog","f25X_d5_rg8_2_wog","f25X_d5_rg8_3_wog"]}
{"assemblies_lengths":[4649001,4638443,4647261,4661578,4648404,4654462,4647823,4649251,4648711,4648069],"filenames":["f25X_d5_all_wog","f25X_d5_rg4_1_wog","f25X_d5_rg4_2_wog","f25X_d5_rg4_3_wog","f25X_d5_rg6_1_wog","f25X_d5_rg6_2_wog","f25X_d5_rg6_3_wog","f25X_d5_rg8_1_wog","f25X_d5_rg8_2_wog","f25X_d5_rg8_3_wog"]}
{"reflen":4639675}
{"ref_genes_number":4497,"genes_in_contigs":{"f25X_d5_rg4_1_wog":[3508,750,202,28],"f25X_d5_all_wog":[4494],"f25X_d5_rg4_3_wog":[3635,385,210,107,118,37],"f25X_d5_rg4_2_wog":[4494],"f25X_d5_rg8_1_wog":[4494],"f25X_d5_rg8_3_wog":[4494],"f25X_d5_rg8_2_wog":[4494],"f25X_d5_rg6_3_wog":[4494],"f25X_d5_rg6_2_wog":[4495],"f25X_d5_rg6_1_wog":[4494]},"filenames":["f25X_d5_all_wog","f25X_d5_rg4_1_wog","f25X_d5_rg4_2_wog","f25X_d5_rg4_3_wog","f25X_d5_rg6_1_wog","f25X_d5_rg6_2_wog","f25X_d5_rg6_3_wog","f25X_d5_rg8_1_wog","f25X_d5_rg8_2_wog","f25X_d5_rg8_3_wog"]}
{{ 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.