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better","values":[0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0],"isMain":false},{"metricName":"# structural variations","quality":"Less is better","values":[0],"isMain":false},{"metricName":"# unaligned mis. contigs","quality":"Less is better","values":[6],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[3],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[1868],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[85],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[68062],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["7401.77"],"isMain":true},{"metricName":"# mismatches","quality":"Less is better","values":[57881],"isMain":false},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["195.40"],"isMain":true},{"metricName":"# indels","quality":"Less is better","values":[1528],"isMain":false},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[1450],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[78],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[4248],"isMain":false},{"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":[1246],"isMain":true},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[212],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[2415],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[980906],"isMain":true},{"metricName":"Total 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fragments","quality":"Equal","values":[4],"isMain":false},{"metricName":"Reference GC (%)","quality":"Equal","values":["51.08"],"isMain":false},{"metricName":"# total reads","quality":"Equal","values":[2193472],"isMain":false},{"metricName":"# left","quality":"Equal","values":["1096736"],"isMain":false},{"metricName":"# right","quality":"Equal","values":["1096736"],"isMain":false},{"metricName":"# reference mapped","quality":"Equal","values":["98359"],"isMain":false},{"metricName":"Reference mapped (%)","quality":"Equal","values":[4.48],"isMain":false},{"metricName":"# reference properly paired","quality":"Equal","values":["91356"],"isMain":false},{"metricName":"Reference properly paired (%)","quality":"Equal","values":[4.16],"isMain":false},{"metricName":"# reference singletons","quality":"Equal","values":["2523"],"isMain":false},{"metricName":"Reference singletons (%)","quality":"Equal","values":[0.12],"isMain":false},{"metricName":"# reference misjoint 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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.",
"# 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.