Loading...
{"date":"26 April 2024, Friday, 12:22:11","assembliesNames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"],"referenceName":"nCoV-2019.reference","order":[0,1,2],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["96.010","98.987","98.973"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.002","1.000","1.004"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["14 + 9 part","19 + 5 part","19 + 5 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[10408,20951,16899],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[28764,29600,29723],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[4093,20973,16925],"isMain":false},{"metricName":"NG90","quality":"More is better","values":[4051,8774,5513],"isMain":false},{"metricName":"auNG","quality":"More is better","values":["6611.6","18300.6","13750.6"],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[4093,20951,8650],"isMain":false},{"metricName":"NA90","quality":"More is better","values":[null,null,null],"isMain":false},{"metricName":"auNA","quality":"More is better","values":["5252.5","14570.3","10678.3"],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[4093,20951,16899],"isMain":true},{"metricName":"NGA90","quality":"More is better","values":[1913,8649,4174],"isMain":false},{"metricName":"auNGA","quality":"More is better","values":["6013.4","17180.5","12634.9"],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[3,1,1],"isMain":false},{"metricName":"LG90","quality":"Less is better","values":[5,2,3],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[3,1,2],"isMain":false},{"metricName":"LA90","quality":"Less is better","values":[null,null,null],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[3,1,1],"isMain":true},{"metricName":"LGA90","quality":"Less is better","values":[6,2,3],"isMain":false}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0,0,0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0,0,0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":"# scaffold gap ext. mis.","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":"# unaligned mis. contigs","quality":"Less is better","values":[0,0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[3,1,1],"isMain":false},{"metricName":"Fully unaligned length","quality":"Less is better","values":[5432,5513,5513],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[0,0,0],"isMain":false}]],["Mismatches",[{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["38.24","20.27","10.09"],"isMain":true},{"metricName":"# mismatches","quality":"Less is better","values":[11,6,3],"isMain":false},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["3.48","0.00","0.00"],"isMain":true},{"metricName":"# indels","quality":"Less is better","values":[1,0,0],"isMain":false},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[1,0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[1,0,0],"isMain":false},{"metricName":"# N's per 100 kbp","quality":"Less is better","values":["0.00","0.00","0.00"],"isMain":true},{"metricName":"# N's","quality":"Less is better","values":[0,0,0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[9,3,4],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[13,5,5],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[7,3,4],"isMain":false},{"metricName":"# contigs (>= 5000 bp)","quality":"Equal","values":[1,3,3],"isMain":false},{"metricName":"# contigs (>= 10000 bp)","quality":"Equal","values":[1,1,1],"isMain":false},{"metricName":"# contigs (>= 25000 bp)","quality":"Equal","values":[0,0,0],"isMain":false},{"metricName":"# contigs (>= 50000 bp)","quality":"Equal","values":[0,0,0],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[10409,20973,16925],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[34235,35260,35382],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[36064,36164,35820],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[32873,35260,35382],"isMain":true},{"metricName":"Total length (>= 5000 bp)","quality":"More is better","values":[10409,35260,31208],"isMain":false},{"metricName":"Total length (>= 10000 bp)","quality":"More is better","values":[10409,20973,16925],"isMain":true},{"metricName":"Total length (>= 25000 bp)","quality":"More is better","values":[0,0,0],"isMain":false},{"metricName":"Total length (>= 50000 bp)","quality":"More is better","values":[0,0,0],"isMain":true},{"metricName":"N50","quality":"More is better","values":[4093,20973,8770],"isMain":false},{"metricName":"N90","quality":"More is better","values":[3823,5513,4174],"isMain":false},{"metricName":"auN","quality":"More is better","values":["5775.0","15520.2","11621.3"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[3,1,2],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[6,3,4],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["39.18","39.05","39.06"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[{"metricName":"# similar correct contigs","quality":"Equal","values":[0,0,0],"isMain":false},{"metricName":"# similar misassembled blocks","quality":"Equal","values":[0,0,0],"isMain":false}]],["Reference statistics",[{"metricName":"Reference length","quality":"Equal","values":[29903,29903,29903],"isMain":false},{"metricName":"Reference fragments","quality":"Equal","values":[1,1,1],"isMain":false},{"metricName":"Reference GC (%)","quality":"Equal","values":["37.97","37.97","37.97"],"isMain":false},{"metricName":"Reference genomic features","quality":"Equal","values":[24,24,24],"isMain":false}]]],"subreferences":[],"subreports":[],"minContig":500}
{{ qualities }}
{{ mainMetrics }}
{"filenames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"],"lists_of_lengths":[[10409,4514,4093,4070,4051,3823,1913,845,517],[20973,8774,5513],[16925,8770,5513,4174]]}
{"filenames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"],"assemblies_lengths":[34235,35260,35382]}
{"reflen":[29903]}
{"tickX":1}
{"coord_x":[[0.0,1e-10,30.40455674017818,30.404556740278178,43.589893383963776,43.58989338406378,55.54549437709946,55.54549437719946,67.43391266247991,67.43391266257991,79.26683218927998,79.26683218937998,90.43376661311524,90.43376661321524,96.02161530597341,96.02161530607341,98.48984956915437,98.48984956925437,100.0,100.0000000001],[0.0,1e-10,59.480998298355075,59.48099829845508,84.36471922858763,84.36471922868763,100.0,100.0000000001],[0.0,1e-10,47.83505737380589,47.83505737390589,72.6216720366288,72.6216720367288,88.20304109434176,88.20304109444176,100.0,100.0000000001]],"coord_y":[[10409,10409,10409,4514,4514,4093,4093,4070,4070,4051,4051,3823,3823,1913,1913,845,845,517,517,0.0],[20973,20973,20973,8774,8774,5513,5513,0.0],[16925,16925,16925,8770,8770,5513,5513,4174,4174,0.0]],"filenames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"]}
{"coord_x":[[0.0,1e-10,34.80921646657526,34.80921646667526,49.904691836939435,49.90469183703944,63.59228171086513,63.59228171096513,77.20295622512792,77.20295622522792,90.75009196401699,90.75009196411699,103.53476239842156,103.53476239852156,109.9321138347323,109.93211383483231,112.75791726582617,112.75791726592617,114.4868407852055,114.4868407853055],[0.0,1e-10,70.13677557435709,70.13677557445709,99.47831321272113,99.47831321282113,117.91459050931344,117.91459050941344],[0.0,1e-10,56.59967227368492,56.59967227378492,85.92783332775976,85.92783332785976,104.36411062435207,104.36411062445207,118.3225763301341,118.3225763302341]],"coord_y":[[10409,10409,10409,4514,4514,4093,4093,4070,4070,4051,4051,3823,3823,1913,1913,845,845,517,517,0.0],[20973,20973,20973,8774,8774,5513,5513,0.0],[16925,16925,16925,8770,8770,5513,5513,4174,4174,0.0]],"filenames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"]}
{"coord_x":[[0.0,1e-10,30.401635752884474,30.401635752984472,43.54023659997079,43.54023660007079,55.49583759310647,55.495837593206474,67.26449539944501,67.26449539954501,78.43142982328027,78.43142982338027,84.01927851613846,84.01927851623846],[0.0,1e-10,59.41860465116279,59.41860465126279,83.94781622234827,83.94781622244827],[0.0,1e-10,47.76157368153298,47.76157368163298,72.20903284155786,72.20903284165786,84.0059917472161,84.0059917473161]],"coord_y":[[10408,10408,10408,4498,4498,4093,4093,4029,4029,3823,3823,1913,1913,0.0],[20951,20951,20951,8649,8649,0.0],[16899,16899,16899,8650,8650,4174,4174,0.0]],"filenames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"]}
{"coord_x":[[0.0,1e-10,34.80587232050296,34.80587232060296,49.84784135371033,49.84784135381033,63.535431227636025,63.53543122773603,77.00899575293448,77.00899575303448,89.79366618733906,89.79366618743906,96.1910176236498,96.1910176237498],[0.0,1e-10,70.06320436076648,70.06320436086648,98.98672374009297,98.98672374019297],[0.0,1e-10,56.5127244758051,56.5127244759051,85.43958800120389,85.43958800130389,99.39805370698592,99.39805370708592]],"coord_y":[[10408,10408,10408,4498,4498,4093,4093,4029,4029,3823,3823,1913,1913,0.0],[20951,20951,20951,8649,8649,0.0],[16899,16899,16899,8650,8650,4174,4174,0.0]],"filenames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"]}
{"coord_x":[[0,1],[0,1],[0,1]],"coord_y":[[96.1910176236498,96.1910176236498],[98.98672374009297,98.98672374009297],[99.39805370698592,99.39805370698592]],"filenames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"]}
{"filenames":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"],"features_in_contigs":{"SAMPLE2_PE.scaffolds":[0,0,0,0,14,0,0,0,0],"SAMPLE1_PE.scaffolds":[19,0,0],"SAMPLE3_SE.scaffolds":[19,0,0,0]},"ref_features_number":24}
{{ 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":["SAMPLE2_PE.scaffolds","SAMPLE1_PE.scaffolds","SAMPLE3_SE.scaffolds"],"reference_index":3,"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],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,1,2,3,2,11,15,21,17,33,9,28,22,28,21,16,22,14,13,13,9,10,9,5,3,3,5,0,1,1,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,2,2,4,2,10,21,11,19,33,24,32,18,19,21,23,15,15,16,21,5,13,10,3,2,2,4,2,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[0.0,1.0,2.0,3.0,4.0,5.0,6.0,7.0,8.0,9.0,10.0,11.0,12.0,13.0,14.0,15.0,16.0,17.0,18.0,19.0,20.0,21.0,22.0,23.0,24.0,25.0,26.0,27.0,28.0,29.0,30.0,31.0,32.0,33.0,34.0,35.0,36.0,37.0,38.0,39.0,40.0,41.0,42.0,43.0,44.0,45.0,46.0,47.0,48.0,49.0,50.0,51.0,52.0,53.0,54.0,55.0,56.0,57.0,58.0,59.0,60.0,61.0,62.0,63.0,64.0,65.0,66.0,67.0,68.0,69.0,70.0,71.0,72.0,73.0,74.0,75.0,76.0,77.0,78.0,79.0,80.0,81.0,82.0,83.0,84.0,85.0,86.0,87.0,88.0,89.0,90.0,91.0,92.0,93.0,94.0,95.0,96.0,97.0,98.0,99.0,100.0],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,5,2,8,8,13,16,9,33,30,29,21,27,16,25,23,10,11,16,14,10,8,6,3,3,4,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]],[[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]]],"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],[0,0,0,0,0,0,0,4,3,1,1,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,2,1,0,0,0,0,0,0,0,0,0,0,0,0]],[[0,5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100],[0,0,0,0,0,0,0,3,1,0,0,0,0,0,0,0,0,0,0,0,0]]],"lists_of_gc_info":null}
{"links":["icarus_viewers/alignment_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.