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{"date":"19 February 2019, Tuesday, 15:50:33","assembliesNames":["Pgenerosa_v071"],"referenceName":"","order":[0],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N's","quality":"Less is better","values":[199621370],"isMain":false},{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["14282.86"],"isMain":true}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[14014],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[14014],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[14014],"isMain":false},{"metricName":"# contigs (>= 5000 bp)","quality":"Equal","values":[14014],"isMain":false},{"metricName":"# contigs (>= 10000 bp)","quality":"Equal","values":[14014],"isMain":false},{"metricName":"# contigs (>= 25000 bp)","quality":"Equal","values":[2028],"isMain":false},{"metricName":"# contigs (>= 50000 bp)","quality":"Equal","values":[251],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[89643857],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[1397628576],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[1397628576],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[1397628576],"isMain":true},{"metricName":"Total length (>= 5000 bp)","quality":"More is better","values":[1397628576],"isMain":false},{"metricName":"Total length (>= 10000 bp)","quality":"More is better","values":[1397628576],"isMain":true},{"metricName":"Total length (>= 25000 bp)","quality":"More is better","values":[1225810181],"isMain":false},{"metricName":"Total length (>= 50000 bp)","quality":"More is better","values":[1166200614],"isMain":true},{"metricName":"N50","quality":"More is better","values":[45393038],"isMain":false},{"metricName":"N75","quality":"More is better","values":[12042408],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[12],"isMain":false},{"metricName":"L75","quality":"Less is better","values":[24],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["33.75"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500}
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{{ 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 }}
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{"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.",
"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.