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[{"date":"03 April 2019, Wednesday, 15:26:51","assembliesNames":["MG1_ets","MG1_sjw","MG2_ets","MG2_sjw","MG3_ets","MG3_sjw","MG5_ets","MG5_sjw","MG6_ets","MG6_sjw","MG7_ets","MG7_sjw"],"referenceName":"combined_reference","order":[0,1,2,3,4,5,6,7,8,9,10,11],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["63.202","75.446","45.452","56.867","39.548","46.910","30.724","39.276","69.194","81.770","62.267","80.959"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.189","1.353","1.154","1.270","1.150","1.243","1.105","1.113","1.201","1.368","1.136","1.283"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[7851,29599,4290,33804,4025,37919,4627,41962,7657,40667,6491,33492],"isMain":true},{"metricName":"Total aligned length","quality":"More is 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s_DSM_19645___NX02","Sphingomonas_sp._ERG5","Sphingomonas_taxi","Sphingopyxis_sp._MC1","Spongiibacter_tropicus","Stanieria_cyanosphaera_PCC_7437","Stenotrophomonas_maltophilia_JV3","Stenotrophomonas_sp._RIT309","Streptococcus_agalactiae_SS1219","Streptococcus_sanguinis_SK115","Streptomyces_albulus","Streptomyces_indicus","Streptomyces_mobaraensis_NBRC_13819___DSM_40847","Sulfitobacter_sp._EE_36","Sulfitobacter_sp._NAS_14.1","Tenacibaculum_gallaicum","Tenacibaculum_maritimum","Tenacibaculum_skagerrakense","Thalassobaculum_salexigens_DSM_19539","Thalassospira_profundimaris","Thalassospira_xiamenensis_M_5___DSM_17429","Thermoplasma_acidophilum","Thermoplasmatales_archaeon_E_plasma","Thioalkalivibrio_sulfidiphilus_HL_EbGr7","Thioflavicoccus_mobilis","Thiogranum_longum","Thiohalobacter_thiocyanaticus","Thiorhodococcus_drewsii_AZ1","Thiorhodococcus_sp._AK35","Tistrella_mobilis","Tistrella_mobilis_KA081020_065","Tolypothrix_campylonemoides_VB511288","Umboniibacter_marinipuniceus","Verrucosispora_maris_AB_18_032","Vibrio_lentus","Vitreoscilla_stercoraria_DSM_513","Xanthobacter_autotrophicus_Py2","Xanthomonas_translucens_pv._graminis","Xenococcus_sp._PCC_7305","Zea_mays","Zhouia_amylolytica_AD3","Zooshikella_ganghwensis_DSM_15267","alpha_proteobacterium_SCGC_AAA076_C03","bacterium_DY22613","bacterium_KD52","endosymbiont_of_Ridgeia_piscesae","gamma_proteobacterium_SCGC_AB_629_P17","marine_gamma_proteobacterium_HTCC2080","mine_drainage_metagenome","unidentified_eubacterium_SCB49"],"subreports":[[["Genome 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{"links":["icarus.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.