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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":["ABySS_k96","ABySS_k128","a5-miseq","velvetopt_data_97"],"minContig":500,"report":[["Genome statistics",[{"values":["99.820","99.865","99.477","99.273","99.346","99.251","99.262","99.733","99.413"],"quality":"More is better","isMain":true,"metricName":"Genome fraction (%)"},{"values":["1.008","1.008","1.001","1.001","1.000","1.000","1.000","1.002","1.003"],"quality":"Less is better","isMain":true,"metricName":"Duplication ratio"},{"values":[371505,371505,460304,439873,459976,439828,439855,207812,242670],"quality":"More is better","isMain":true,"metricName":"Largest alignment"},{"values":[3330166,3331499,3297745,3288817,3289822,3287166,3287722,3309669,3302292],"quality":"More is better","isMain":true,"metricName":"Total aligned length"},{"values":[142571,189671,247335,139304,248333,181509,180386,65312,116791],"quality":"More is better","isMain":false,"metricName":"NG50"},{"values":[80451,106281,170408,103933,170204,79346,116610,38126,71618],"quality":"More is better","isMain":false,"metricName":"NG75"},{"values":[142571,189671,247335,139304,248333,181509,180386,63821,120995],"quality":"More is better","isMain":false,"metricName":"NA50"},{"values":[80451,106281,170371,103812,170204,105340,116610,38126,71618],"quality":"More is better","isMain":false,"metricName":"NA75"},{"values":[142571,189671,247335,139304,248333,181509,180386,63821,116791],"quality":"More is better","isMain":true,"metricName":"NGA50"},{"values":[80451,106281,170371,103812,170204,79258,116610,38126,71618],"quality":"More is better","isMain":false,"metricName":"NGA75"},{"values":[8,7,5,8,5,6,6,15,10],"quality":"Less is better","isMain":false,"metricName":"LG50"},{"values":[15,13,9,14,9,13,11,32,18],"quality":"Less is better","isMain":false,"metricName":"LG75"},{"values":[8,7,5,8,5,6,6,16,9],"quality":"Less is better","isMain":false,"metricName":"LA50"},{"values":[15,13,9,14,9,12,11,33,18],"quality":"Less is better","isMain":false,"metricName":"LA75"},{"values":[8,7,5,8,5,6,6,16,10],"quality":"Less is better","isMain":true,"metricName":"LGA50"},{"values":[15,13,9,14,9,13,11,33,18],"quality":"Less is better","isMain":false,"metricName":"LGA75"}]],["Misassemblies",[{"values":[0,0,1,0,0,0,0,4,0],"quality":"Less is better","isMain":true,"metricName":"# misassemblies"},{"values":[0,0,1,0,0,0,0,2,0],"quality":"Less is better","isMain":false,"metricName":" # relocations"},{"values":[0,0,0,0,0,0,0,2,0],"quality":"Less is better","isMain":false,"metricName":" # translocations"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":" # inversions"},{"values":[0,0,1,0,0,0,0,4,0],"quality":"Less is better","isMain":false,"metricName":"# misassembled contigs"},{"values":[0,0,267106,0,0,0,0,365987,0],"quality":"Less is better","isMain":true,"metricName":"Misassembled contigs length"},{"values":[1,0,1,0,0,0,0,4,0],"quality":"Less is better","isMain":false,"metricName":"# local misassemblies"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# unaligned mis. contigs"}]],["Unaligned",[{"values":[0,0,0,0,2,0,0,0,1],"quality":"Less is better","isMain":false,"metricName":"# fully unaligned contigs"},{"values":[0,0,0,0,1089,0,0,0,520],"quality":"Less is better","isMain":false,"metricName":"Fully unaligned length"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"# partially unaligned contigs"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Less is better","isMain":false,"metricName":"Partially unaligned length"}]],["Mismatches",[{"values":[7,5,7,2,7,4,3,25,4],"quality":"Less is better","isMain":false,"metricName":"# mismatches"},{"values":[15,15,22,13,17,17,15,14,38],"quality":"Less is better","isMain":false,"metricName":"# indels"},{"values":[39,119,176,28,104,143,95,68,54],"quality":"Less is better","isMain":false,"metricName":"Indels length"},{"values":["0.21","0.15","0.21","0.06","0.21","0.12","0.09","0.76","0.12"],"quality":"Less is better","isMain":true,"metricName":"# mismatches per 100 kbp"},{"values":["0.45","0.45","0.67","0.40","0.52","0.52","0.46","0.42","1.15"],"quality":"Less is better","isMain":true,"metricName":"# indels per 100 kbp"},{"values":[12,11,15,11,13,13,12,9,36],"quality":"Less is better","isMain":false,"metricName":" # indels (<= 5 bp)"},{"values":[3,4,7,2,4,4,3,5,2],"quality":"Less is better","isMain":false,"metricName":" # indels (> 5 bp)"},{"values":[238,95,29,0,0,270,0,8,0],"quality":"Less is better","isMain":false,"metricName":"# N's"},{"values":["7.14","2.85","0.88","0.00","0.00","8.21","0.00","0.24","0.00"],"quality":"Less is better","isMain":true,"metricName":"# N's per 100 kbp"}]],["Statistics without reference",[{"values":[43,36,29,41,26,37,35,86,78],"quality":"Equal","isMain":true,"metricName":"# contigs"},{"values":[52,45,29,83,44,48,57,86,189],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 0 bp)"},{"values":[42,36,24,40,23,36,34,83,61],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 1000 bp)"},{"values":[37,33,18,30,19,31,24,71,42],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 5000 bp)"},{"values":[34,31,17,28,18,29,23,62,39],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 10000 bp)"},{"values":[27,23,16,25,17,24,20,42,29],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 25000 bp)"},{"values":[21,20,14,21,15,21,18,25,23],"quality":"Equal","isMain":false,"metricName":"# contigs (>= 50000 bp)"},{"values":[371505,371505,460304,439873,459976,439828,439855,207813,242670],"quality":"More is better","isMain":true,"metricName":"Largest contig"},{"values":[3331667,3331593,3297786,3290098,3290913,3287449,3287724,3309777,3303020],"quality":"More is better","isMain":true,"metricName":"Total length"},{"values":[3333623,3334167,3297786,3302864,3297390,3290412,3294507,3309777,3341618],"quality":"More is better","isMain":false,"metricName":"Total length (>= 0 bp)"},{"values":[3330672,3331593,3294340,3289376,3289008,3286633,3286908,3307250,3293078],"quality":"More is better","isMain":true,"metricName":"Total length (>= 1000 bp)"},{"values":[3314497,3320081,3276990,3262440,3278167,3274486,3260140,3267705,3246906],"quality":"More is better","isMain":false,"metricName":"Total length (>= 5000 bp)"},{"values":[3289458,3303922,3270720,3249183,3271897,3261862,3253870,3196926,3225949],"quality":"More is better","isMain":true,"metricName":"Total length (>= 10000 bp)"},{"values":[3172423,3166177,3253349,3204771,3259206,3183316,3200922,2827267,3070921],"quality":"More is better","isMain":false,"metricName":"Total length (>= 25000 bp)"},{"values":[2927072,3021896,3158299,3034363,3165087,3061935,3106884,2232371,2824294],"quality":"More is better","isMain":true,"metricName":"Total length (>= 50000 bp)"},{"values":[142571,189671,247335,139304,248333,181509,180386,65312,120995],"quality":"More is better","isMain":false,"metricName":"N50"},{"values":[80451,106281,170408,103933,170204,105340,116610,38126,71618],"quality":"More is better","isMain":false,"metricName":"N75"},{"values":[8,7,5,8,5,6,6,15,9],"quality":"Less is better","isMain":false,"metricName":"L50"},{"values":[15,13,9,14,9,12,11,32,18],"quality":"Less is better","isMain":false,"metricName":"L75"},{"values":["57.19","57.19","57.23","57.24","57.24","57.24","57.24","57.23","57.24"],"quality":"Equal","isMain":false,"metricName":"GC (%)"}]],["Predicted genes",[{"values":[3218,3219,3228,3223,3217,3214,3212,3252,3264],"quality":"More is better","isMain":true,"metricName":"# predicted genes (unique)"},{"values":[3237,3237,3232,3225,3218,3215,3214,3261,3267],"quality":"More is better","isMain":false,"metricName":"# predicted genes (>= 0 bp)"},{"values":[2851,2854,2842,2842,2843,2839,2834,2850,2860],"quality":"More is better","isMain":false,"metricName":"# predicted genes (>= 300 bp)"},{"values":[344,344,344,345,344,344,344,343,343],"quality":"More is better","isMain":false,"metricName":"# predicted genes (>= 1500 bp)"},{"values":[34,34,34,33,34,34,34,34,34],"quality":"More is better","isMain":false,"metricName":"# predicted genes (>= 3000 bp)"}]],["Similarity statistics",[{"values":[14,14,13,15,14,17,15,2,15],"quality":"Equal","isMain":false,"metricName":"# similar correct contigs"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Equal","isMain":false,"metricName":"# similar misassembled blocks"}]],["Reference statistics",[{"values":[3310727,3310727,3310727,3310727,3310727,3310727,3310727,3310727,3310727],"quality":"Equal","isMain":false,"metricName":"Reference length"},{"values":[2,2,2,2,2,2,2,2,2],"quality":"Equal","isMain":false,"metricName":"Reference fragments"},{"values":["57.22","57.22","57.22","57.22","57.22","57.22","57.22","57.22","57.22"],"quality":"Equal","isMain":false,"metricName":"Reference GC (%)"},{"values":[0,0,0,0,0,0,0,0,0],"quality":"Equal","isMain":false,"metricName":"Reference genes"}]]],"referenceName":"520466.6","date":"28 June 2017, Wednesday, 20:29:13","order":[0,1,2,3,4,5,6,7,8],"assembliesNames":["ABySS_k96","ABySS_k128","a5-miseq","megahit","SPAdes_def","velvetopt_data_97","idba_ud","omega","sga"]}
{{ qualities }}
{{ mainMetrics }}
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{"reflen":[2122766,1187961]}
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{{ genesInContigs }}
{{ operonsInContigs }}
[{{ num_contigs }},
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{{ 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.