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{"subreports":[],"report":[["Genome statistics",[{"values":["1.729"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.145"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":["0 + 6 part"],"quality":"More is better","isMain":true,"metricName":"# genomic features"},{"values":[517],"quality":"More is better","isMain":true,"metricName":"Largest alignment"},{"values":[517],"quality":"More is better","isMain":true,"metricName":"Total aligned length"},{"values":[1380],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[1093],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[null],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[9],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[15],"quality":"Less is better","isMain":false,"metricName":"LG75"}]],["Reads mapping",[]],["Misassemblies",[{"values":[0],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[0],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# scaffold gap ext. mis."},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# scaffold gap loc. mis."},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# unaligned mis. contigs"}]],["Unaligned",[{"values":[65],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[58650],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.00"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.00"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # indels (<= 5 bp)"},{"values":[0],"quality":"Less is better","isMain":false,"metricName":" # indels (> 5 bp)"},{"values":[75],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["126.60"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Statistics without reference",[{"values":[66],"quality":"Equal","isMain":true,"metricName":"# contigs"},{"values":[541],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[16],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[0],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 5000 bp)"},{"values":[0],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 10000 bp)"},{"values":[0],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 25000 bp)"},{"values":[0],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 50000 bp)"},{"values":[2877],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[59242],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[163765],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[24443],"quality":"More is better","isMain":true,"metricName":"Total length (>= 1000 bp)"},{"values":[0],"quality":"More is better","isMain":false,"metricName":"Total length (>= 5000 bp)"},{"values":[0],"quality":"More is better","isMain":true,"metricName":"Total length (>= 10000 bp)"},{"values":[0],"quality":"More is better","isMain":false,"metricName":"Total length (>= 25000 bp)"},{"values":[0],"quality":"More is better","isMain":true,"metricName":"Total length (>= 50000 bp)"},{"values":[942],"quality":"More is better","isMain":false,"metricName":"N50"},{"values":[680],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[22],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[41],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["46.83"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[{"values":[0],"quality":"Equal","isMain":false,"metricName":"# similar correct contigs"},{"values":[0],"quality":"Equal","isMain":false,"metricName":"# similar misassembled blocks"}]],["Reference statistics",[{"values":[29903],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":[1],"quality":"Equal","isMain":false,"metricName":"Reference fragments"},{"values":["37.97"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[59],"quality":"Equal","isMain":false,"metricName":"Reference genomic features"}]]],"referenceName":"NC_045512.2","date":"14 May 2021, Friday, 16:36:03","subreferences":[],"minContig":500,"order":[0],"assembliesNames":["CV29_velvet_contigs"]}
{{ qualities }}
{{ mainMetrics }}
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{"assemblies_lengths":[59242],"filenames":["CV29_velvet_contigs"]}
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{"features_in_contigs":{"CV29_velvet_contigs":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]},"ref_features_number":59,"filenames":["CV29_velvet_contigs"]}
{{ 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 }}
{"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],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,1,3,3,6,2,5,6,6,7,17,14,22,19,27,22,37,34,53,34,44,26,37,24,21,31,18,15,14,10,15,2,9,1,0,2,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[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]]],"reference_index":1,"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],[0,0,0,0,0,0,1,4,21,21,16,3,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null,"filenames":["CV29_velvet_contigs"]}
{"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.",
"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.