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Contigs are ordered from largest (contig #1) to smallest. Contigs are broken into nonoverlapping 100 bp windows. Plot shows numbers of windows for each GC percentage. |
{"assembliesWithNs":["Geneious"],"minContig":500,"report":[["Genome statistics",[{"values":["99.527","97.174","99.589","8.487","99.589","96.525","99.743","93.799","94.737","99.589","99.155"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.000","1.006","1.004","1.151","1.323","1.000","1.000","1.001","1.001","1.027","1.020"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":[30946,16305,31106,1517,38103,16092,31013,16048,16196,31552,31461],"quality":"More is better","isMain":true,"metricName":"Largest alignment"},{"values":[30946,30401,31106,2900,40923,30012,31013,29219,29511,31552,31461],"quality":"More is better","isMain":true,"metricName":"Total aligned length"},{"values":[30965,16305,31106,null,40990,16092,31020,16048,16196,31829,32871],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[30965,5625,31106,null,40990,10831,31020,11640,11970,31829,32871],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[30946,16305,31106,1123,38103,16092,31013,10553,5582,31552,31461],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[30946,5625,31106,1123,38103,10831,31013,null,null,31552,31461],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[30946,16305,31106,null,38103,16092,31013,16048,16196,31552,31461],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[30946,5625,31106,null,38103,10831,31013,10553,5027,31552,31461],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[1,1,1,null,1,1,1,1,1,1,1],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[1,3,1,null,1,2,1,2,2,1,1],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[1,1,1,2,1,1,1,2,2,1,1],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[1,3,1,2,1,2,1,null,null,1,1],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[1,1,1,null,1,1,1,1,1,1,1],"quality":"Less is better","isMain":true,"metricName":"LGA50"},{"values":[1,3,1,null,1,2,1,2,3,1,1],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Misassemblies",[{"values":[0,0,0,1,3,0,0,0,0,0,0],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[0,0,0,0,2,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,0,1,1,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[0,0,0,1,1,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[0,0,0,1481,40990,0,0,0,0,0,0],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[1,1,1,1,1,1,0,1,1,2,2],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"},{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# unaligned mis. contigs"}]],["Unaligned",[{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0,0,0,2,2,0,1],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0,0,0,11110,11632,0,1410],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[27,27,27,0,5,25,27,28,28,21,153],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[10,10,10,0,1,10,10,12,12,4,40],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[17,17,17,0,1,17,17,19,19,5,51],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["87.21","89.32","87.16","0.00","16.14","83.26","87.02","95.97","95.02","67.79","496.06"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["32.30","33.08","32.28","0.00","3.23","33.31","32.23","41.13","40.72","12.91","129.69"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[10,10,10,0,1,10,10,12,12,4,40],"quality":"Less is better","isMain":false,"metricName":" # indels (<= 5 bp)"},{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # indels (> 5 bp)"},{"values":[0,0,0,0,0,0,0,0,0,0,778],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["0.00","0.00","0.00","0.00","0.00","0.00","0.00","0.00","0.00","0.00","2366.83"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Statistics without reference",[{"values":[1,5,1,2,1,3,1,4,5,1,1],"quality":"Equal","isMain":true,"metricName":"# contigs"},{"values":[1,5,1,2,1,3,1,4,5,1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[1,5,1,2,1,3,1,4,5,1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[1,3,1,0,1,2,1,3,4,1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 5000 bp)"},{"values":[1,1,1,0,1,2,1,3,2,1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 10000 bp)"},{"values":[1,0,1,0,1,0,1,0,0,1,1],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 25000 bp)"},{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 50000 bp)"},{"values":[30965,16305,31106,1557,40990,16092,31020,16048,16196,31829,32871],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[30965,30401,31106,3038,40990,30012,31020,40329,41143,31829,32871],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[30965,30401,31106,3038,40990,30012,31020,40329,41143,31829,32871],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[30965,30401,31106,3038,40990,30012,31020,40329,41143,31829,32871],"quality":"More is better","isMain":true,"metricName":"Total length (>= 1000 bp)"},{"values":[30965,27558,31106,0,40990,26923,31020,39135,39861,31829,32871],"quality":"More is better","isMain":false,"metricName":"Total length (>= 5000 bp)"},{"values":[30965,16305,31106,0,40990,26923,31020,39135,28166,31829,32871],"quality":"More is better","isMain":true,"metricName":"Total length (>= 10000 bp)"},{"values":[30965,0,31106,0,40990,0,31020,0,0,31829,32871],"quality":"More is better","isMain":false,"metricName":"Total length (>= 25000 bp)"},{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"More is better","isMain":true,"metricName":"Total length (>= 50000 bp)"},{"values":[30965,16305,31106,1557,40990,16092,31020,11640,11970,31829,32871],"quality":"More is better","isMain":false,"metricName":"N50"},{"values":[30965,5625,31106,1481,40990,10831,31020,11447,6113,31829,32871],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[1,1,1,1,1,1,1,2,2,1,1],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[1,3,1,2,1,2,1,3,3,1,1],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["36.18","36.21","36.19","36.21","35.80","36.20","36.19","35.57","35.57","36.10","35.73"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Predicted genes",[]],["Similarity statistics",[{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"Equal","isMain":false,"metricName":"# similar correct contigs"},{"values":[0,0,0,0,0,0,0,0,0,0,0],"quality":"Equal","isMain":false,"metricName":"# similar misassembled blocks"}]],["Reference statistics",[{"values":[31106,31106,31106,31106,31106,31106,31106,31106,31106,31106,31106],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":[1,1,1,1,1,1,1,1,1,1,1],"quality":"Equal","isMain":false,"metricName":"Reference fragments"},{"values":["36.21","36.21","36.21","36.21","36.21","36.21","36.21","36.21","36.21","36.21","36.21"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"}]]],"referenceName":"Q33_phage","date":"05 July 2018, Thursday, 15:30:41","order":[0,1,2,3,4,5,6,7,8,9,10],"assembliesNames":["CLC","IDBA_UD","MEGAHIT","MIRA","Ray_Meta","SPAdes","SPAdes_meta","SPAdes_sc","SPAdes_sc_careful","VICUNA","Geneious"]}
{{ qualities }}
{{ mainMetrics }}
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{"assemblies_lengths":[30965,30401,31106,3038,40990,30012,31020,40329,41143,31829,32871],"filenames":["CLC","IDBA_UD","MEGAHIT","MIRA","Ray_Meta","SPAdes","SPAdes_meta","SPAdes_sc","SPAdes_sc_careful","VICUNA","Geneious"]}
{"reflen":[31106]}
{"tickX":1}
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{{ genesInContigs }}
{{ 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_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).",
"# 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 (--meta only).",
"# 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.",
"# 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 1 kbp.
- The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.