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+ {"date":"12 April 2023, Wednesday, 09:50:51","assembliesNames":["TEST"],"referenceName":"","order":[0],"report":[["Genome statistics",[{"metricName":"Complete BUSCO (%)","quality":"More is better","values":["0.00"],"isMain":true},{"metricName":"Partial BUSCO (%)","quality":"Less is better","values":["0.00"],"isMain":true}]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00"],"isMain":true},{"metricName":"# N's","quality":"Less is better","values":[0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[62],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[100],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[58],"isMain":false},{"metricName":"# contigs (>= 5000 bp)","quality":"Equal","values":[48],"isMain":false},{"metricName":"# contigs (>= 10000 bp)","quality":"Equal","values":[41],"isMain":false},{"metricName":"# contigs (>= 25000 bp)","quality":"Equal","values":[28],"isMain":false},{"metricName":"# contigs (>= 50000 bp)","quality":"Equal","values":[20],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[436224],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[3017519],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[3027634],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[3015201],"isMain":true},{"metricName":"Total length (>= 5000 bp)","quality":"More is better","values":[2996428],"isMain":false},{"metricName":"Total length (>= 10000 bp)","quality":"More is better","values":[2944723],"isMain":true},{"metricName":"Total length (>= 25000 bp)","quality":"More is better","values":[2735277],"isMain":false},{"metricName":"Total length (>= 50000 bp)","quality":"More is better","values":[2421445],"isMain":true},{"metricName":"N50","quality":"More is better","values":[99915],"isMain":false},{"metricName":"N90","quality":"More is better","values":[27780],"isMain":false},{"metricName":"auN","quality":"More is better","values":["154096.4"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[8],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[28],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["37.31"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500}
+
+
+ {{ qualities }}
+
+
+ {{ mainMetrics }}
+
+
+
+ {"filenames":["TEST"],"lists_of_lengths":[[436224,252900,206370,168397,132811,115359,113419,99915,97190,92075,86662,82418,81741,81694,71911,66886,64537,62649,55461,52826,48115,47790,45935,44497,35306,35051,29358,27780,24296,23952,18776,17346,16026,15602,15587,15306,13750,13168,12357,12074,11206,9892,8939,7812,6929,6828,5969,5336,3276,2262,2083,1817,1775,1642,1578,1526,1515,1299,652,607,534,525]]}
+
+
+ {{ assembliesLengths }}
+
+
+ {{ referenceLength }}
+
+
+ {"tickX":1}
+
+
+ {"coord_x":[[0.0,1e-10,14.45637956215023,14.45637956225023,22.8374369805128,22.837436980612797,29.676499137205102,29.6764991373051,35.25714336844275,35.25714336854275,39.65847439568732,39.65847439578732,43.48144949542986,43.48144949552986,47.24013336784292,47.240133367942924,50.55129727435022,50.55129727445022,53.772155204325145,53.77215520442515,56.82350301688241,56.823503016982414,59.6954650492673,59.6954650493673,62.426781736916986,62.42678173701699,65.13566277461716,65.13566277471716,67.84298624134595,67.84298624144596,70.22610296737155,70.22610296747155,72.44269215869063,72.44269215879063,74.58143594124843,74.58143594134843,76.65761176648763,76.65761176658764,78.49557865252878,78.49557865262878,80.24622214474871,80.24622214484872,81.84074400194332,81.84074400204332,83.42449542156984,83.42449542166985,84.94677249753855,84.94677249763855,86.42139452974448,86.42139452984448,87.59142858752504,87.59142858762505,88.75301199429067,88.75301199439068,89.72593047467142,89.72593047477142,90.64655433818312,90.64655433828312,91.451719110965,91.451719111065,92.24548378982867,92.24548378992867,92.86771682299266,92.86771682309266,93.4425599308571,93.4425599309571,93.97365849229118,93.97365849239118,94.4907057751749,94.4907057752749,95.0072559609401,95.0072559610401,95.5144938606849,95.5144938607849,95.97016621933449,95.97016621943449,96.40655120978526,96.40655120988527,96.81605981602767,96.81605981612768,97.21618985663387,97.21618985673388,97.58755454398133,97.58755454408133,97.91537352374583,97.91537352384583,98.21161026657992,98.21161026667993,98.4704984459087,98.4704984460087,98.7001241748602,98.70012417496021,98.92640278321363,98.92640278331363,99.12421429657941,99.12421429667941,99.30104831154335,99.30104831164336,99.40961432222961,99.40961432232962,99.48457656770347,99.48457656780347,99.5536067875629,99.5536067876629,99.61382181852045,99.61382181862045,99.67264497754613,99.67264497764613,99.72706054212087,99.72706054222087,99.77935515898989,99.77935515908989,99.82992650584802,99.82992650594802,99.88013331481923,99.88013331491923,99.92318192528366,99.92318192538366,99.94478908003562,99.94478908013562,99.964904943432,99.964904943532,99.98260160085157,99.98260160095157,100.0,100.0000000001]],"coord_y":[[436224,436224,436224,252900,252900,206370,206370,168397,168397,132811,132811,115359,115359,113419,113419,99915,99915,97190,97190,92075,92075,86662,86662,82418,82418,81741,81741,81694,81694,71911,71911,66886,66886,64537,64537,62649,62649,55461,55461,52826,52826,48115,48115,47790,47790,45935,45935,44497,44497,35306,35306,35051,35051,29358,29358,27780,27780,24296,24296,23952,23952,18776,18776,17346,17346,16026,16026,15602,15602,15587,15587,15306,15306,13750,13750,13168,13168,12357,12357,12074,12074,11206,11206,9892,9892,8939,8939,7812,7812,6929,6929,6828,6828,5969,5969,5336,5336,3276,3276,2262,2262,2083,2083,1817,1817,1775,1775,1642,1642,1578,1578,1526,1526,1515,1515,1299,1299,652,652,607,607,534,534,525,525,0.0]],"filenames":["TEST"]}
+
+
+ {{ coordNGx }}
+
+
+ {{ coordNAx }}
+
+
+ {{ coordNGAx }}
+
+
+ {{ coordmisassemblies }}
+
+
+ {{ featuresInContigs }}
+
+
+ {{ 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":["TEST"],"reference_index":null,"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],[0,0,0,0,0,0,0,0,1,0,0,1,2,1,1,8,9,12,23,35,61,95,116,157,220,277,347,457,580,713,942,1109,1276,1469,1593,1822,1890,1935,1942,1965,1885,1759,1570,1320,1103,862,701,537,433,295,196,142,95,82,45,30,22,15,10,6,5,1,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]]],"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],[0,0,0,0,0,1,12,44,2,1,2,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null}
+
+
+ {"links":["icarus_viewers/contig_size_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. Similarly, Nx for any x between 0 and 100 could be computed (x% of assembly).",
+ "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. Similarly, NGx for any x between 0 and 100 could be computed (x% of the reference).",
+
+ "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. Similarly, Lx for any x between 0 and 100 could be computed.",
+ "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. Similarly, LGx for any x between 0 and 100 could be computed.",
+
+ "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. Similarly, NAx for any x between 0 and 100 could be computed.",
+ "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. Similarly, NGAx for any x between 0 and 100 could be computed.",
+
+ "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. Similarly, LAx for any x between 0 and 100 could be computed.",
+ "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. Similarly, LGAx for any x between 0 and 100 could be computed.",
+
+ "auN" : "is the area under the Nx curve.",
+ "auNG" : "is the area under the NGx curve.",
+ "auNA" : "is the area under the NAx curve.",
+ "auNGA" : "is the area under the NGAx curve.",
+
+ "Average %IDY" : "is the average of alignment identity percent (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.
