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{"subreports":[],"report":[["Genome statistics",[{"values":["97.797","96.628"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.003","1.004"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":[55106,36102],"quality":"More is better","isMain":true,"metricName":"Largest alignment"},{"values":[58842,58220],"quality":"More is better","isMain":true,"metricName":"Total aligned length"},{"values":[55106,54221],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[55106,54221],"quality":"More is better","isMain":false,"metricName":"NG90"},{"values":["50682.3","49207.2"],"quality":"More is better","isMain":false,"metricName":"auNG"},{"values":[55106,36102],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[55106,18119],"quality":"More is better","isMain":false,"metricName":"NA90"},{"values":["51374.2","28129.6"],"quality":"More is better","isMain":false,"metricName":"auNA"},{"values":[55106,36102],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[55106,18119],"quality":"More is better","isMain":false,"metricName":"NGA90"},{"values":["50671.3","27394.4"],"quality":"More is better","isMain":false,"metricName":"auNGA"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":"LG90"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[1,2],"quality":"Less is better","isMain":false,"metricName":"LA90"},{"values":[1,1],"quality":"Less is better","isMain":true,"metricName":"LGA50"},{"values":[1,2],"quality":"Less is better","isMain":false,"metricName":"LGA90"}]],["Reads mapping",[]],["Misassemblies",[{"values":[0,3],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[0,3],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[1,2],"quality":"Less is better","isMain":false,"metricName":" # interspecies translocations"},{"values":[0,2],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[0,54984],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"# possibly misassembled contigs"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # possible misassemblies"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"},{"values":[1,0],"quality":"Less is better","isMain":false,"metricName":"# scaffold gap ext. mis."},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"# scaffold gap loc. mis."},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"# unaligned mis. contigs"}]],["Unaligned",[{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":["47.59","58.40"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":[28,34],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":["1.70","1.72"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":" # indels (<= 5 bp)"},{"values":[0,0],"quality":"Less is better","isMain":false,"metricName":" # indels (> 5 bp)"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["35.49","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"},{"values":[21,0],"quality":"Less is better","isMain":false,"metricName":"# N's"}]],["Statistics without reference",[{"values":[5,3],"quality":"Equal","isMain":true,"metricName":"# contigs"},{"values":[3,2],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 5000 bp)"},{"values":[1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 10000 bp)"},{"values":[1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 25000 bp)"},{"values":[1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 50000 bp)"},{"values":[55106,54221],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[59178,58431],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[57399,57668],"quality":"More is better","isMain":true,"metricName":"Total length (>= 1000 bp)"},{"values":[55106,54221],"quality":"More is better","isMain":false,"metricName":"Total length (>= 5000 bp)"},{"values":[55106,54221],"quality":"More is better","isMain":true,"metricName":"Total length (>= 10000 bp)"},{"values":[55106,54221],"quality":"More is better","isMain":false,"metricName":"Total length (>= 25000 bp)"},{"values":[55106,54221],"quality":"More is better","isMain":true,"metricName":"Total length (>= 50000 bp)"},{"values":[55106,54221],"quality":"More is better","isMain":false,"metricName":"N50"},{"values":[55106,54221],"quality":"More is better","isMain":false,"metricName":"N90"},{"values":["51385.4","50527.6"],"quality":"More is better","isMain":false,"metricName":"auN"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,1],"quality":"Less is better","isMain":false,"metricName":"L90"},{"values":["50.17","50.11"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[{"values":[0,0],"quality":"Equal","isMain":false,"metricName":"# similar correct contigs"},{"values":[0,0],"quality":"Equal","isMain":false,"metricName":"# similar misassembled blocks"}]],["Reference statistics",[{"values":[59999,59999],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":[1,1],"quality":"Equal","isMain":false,"metricName":"Reference fragments"},{"values":["50.25","50.25"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"}]]],"referenceName":"meta_ref_2","date":"07 July 2023, Friday, 16:03:47","subreferences":[],"minContig":500,"order":[0,1],"assembliesNames":["meta_contigs_1","meta_contigs_2"]}
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{"links_names":["View in Icarus contig browser"],"links":["icarus_viewers/alignment_viewer.html"]}
{
"# 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.