View Source for Saureus 35

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Wiki markup for Saureus 35

{| {{table}} | align="center" style="background:#f0f0f0;"|'''Name''' | align="center" style="background:#f0f0f0;"|'''NumContigs''' | align="center" style="background:#f0f0f0;"|'''NumRefReplicons''' | align="center" style="background:#f0f0f0;"|'''NumAssemblyBases''' | align="center" style="background:#f0f0f0;"|'''NumReferenceBases''' | align="center" style="background:#f0f0f0;"|'''NumLCBs''' | align="center" style="background:#f0f0f0;"|'''DCJ_Distance''' | align="center" style="background:#f0f0f0;"|'''NumDCJBlocks''' | align="center" style="background:#f0f0f0;"|'''NumSNPs''' | align="center" style="background:#f0f0f0;"|'''NumMisCalled''' | align="center" style="background:#f0f0f0;"|'''NumUnCalled''' | align="center" style="background:#f0f0f0;"|'''NumGapsRef''' | align="center" style="background:#f0f0f0;"|'''NumGapsAssembly''' | align="center" style="background:#f0f0f0;"|'''TotalBasesMissed''' | align="center" style="background:#f0f0f0;"|'''PercBasesMissed''' | align="center" style="background:#f0f0f0;"|'''ExtraBases''' | align="center" style="background:#f0f0f0;"|'''PercExtraBases''' | align="center" style="background:#f0f0f0;"|'''MissingChromosomes''' | align="center" style="background:#f0f0f0;"|'''ExtraContigs''' | align="center" style="background:#f0f0f0;"|'''NumSharedBoundaries''' | align="center" style="background:#f0f0f0;"|'''NumInterLcbBoundaries''' | align="center" style="background:#f0f0f0;"|'''BrokenCDS''' | align="center" style="background:#f0f0f0;"|'''IntactCDS''' | align="center" style="background:#f0f0f0;"|'''ContigN50^''' | align="center" style="background:#f0f0f0;"|'''ContigN90''' | align="center" style="background:#f0f0f0;"|'''MinContigLength''' | align="center" style="background:#f0f0f0;"|'''MaxContigLength''' | align="center" style="background:#eee685;"|'''N50^''' | align="center" style="background:#eee685;"|'''blast''' | align="center" style="background:#f0f0f0;"|'''Units(>200)''' | align="center" style="background:#f0f0f0;"|'''N50^''' | align="center" style="background:#f0f0f0;"|'''cor.Units''' | align="center" style="background:#f0f0f0;"|'''cor.N50''' | align="center" style="background:#f0f0f0;"|'''Error,(Indel>=5,Inv,Rel)''' |- | A_S_E_V.m2.ctg.fa.fas||568||2||2769736||2841116||10||560||562||70||70||0||532||403||85722||3.0172||7648||0.2761||0||11||1||5||107||2544||10672||2589||108||42022||11094||2451||515||10549||517||10467||2,(0,0,2) |- | A_S_V_E.m2.ctg.fa.fas||568||2||2768942||2841116||10||560||562||67||67||0||532||402||85728||3.0174||6860||0.2477||0||11||1||5||107||2544||10672||2589||108||42022||11094||2450||515||10549||517||10467||2,(0,0,2) |- | A_V_S_E.m2.ctg.fa.fas||568||2||2768793||2841116||4||560||562||63||63||0||529||401||85334||3.0035||6793||0.2453||0||9||1||1||106||2545||10672||2589||108||42022||11094||2450||515||10549||517||10467||2,(0,0,2) |- | A_E_V_S.m2.ctg.fa.fas||568||2||2768415||2841116||6||562||564||70||70||0||532||407||86175||3.0331||7558||0.273||0||7||1||3||99||2552||10672||2578||108||42022||11094||2449||516||10549||518||10467||2,(0,0,2) |- | E_V_S_A.m2.ctg.fa.fas||568||2||2769559||2841116||7||561||563||72||72||0||532||404||85534||3.0106||7539||0.2722||0||10||1||2||101||2550||10672||2589||108||42022||11094||2450||517||10549||520||10467||3,(1,0,2) |- | E_A_V_S.m2.ctg.fa.fas||568||2||2768415||2841116||8||561||563||90||90||0||528||405||86533||3.0457||7599||0.2745||0||9||1||4||95||2556||10672||2578||108||42022||11094||2449||516||10549||518||10467||2,(0,0,2) |- | S_A_V_E.m2.ctg.fa.fas||568||2||2768941||2841116||4||558||560||84||84||0||527||399||85380||3.0052||6755||0.244||0||11||1||1||107||2544||10672||2589||108||42022||11094||2450||515||10549||517||10467||2,(0,0,2) |- | S_V_E_A.m2.ctg.fa.fas||567||2||2769768||2841116||4||557||559||82||82||0||526||400||85268||3.0012||7470||0.2697||0||11||1||1||107||2544||10672||2589||108||42022||11094||2451||516||10549||518||10467||2,(0,0,2) |- | S_E_V_A.m2.ctg.fa.fas||568||2||2769712||2841116||9||561||563||63||63||0||532||406||85390||3.0055||7536||0.2721||0||11||1||3||97||2554||10672||2578||108||42022||11094||2450||517||10549||519||10467||2,(0,0,2) |- | V_A_E_S.m2.ctg.fa.fas||569||2||2767717||2841116||4||559||561||74||74||0||528||401||86501||3.0446||6652||0.2403||0||11||1||1||106||2545||10672||2589||108||42022||11094||2448||517||10549||519||10467||2,(0,0,2) |- | A_S_E_V.gaa.ctg.fa.fas||974||2||2793850||2841116||4||885||887||152||152||0||822||632||78055||2.7473||13505||0.4834||0||89||1||2||169||2482||7758||1589||100||32731||7796||2349||736||7511||738||7511||3,(0,0,3) |- | A_S_V_E.gaa.ctg.fa.fas||975||2||2794180||2841116||4||887||889||107||107||0||821||632||77989||2.745||13646||0.4884||0||88||1||2||169||2482||7758||1589||100||32731||7796||2349||736||7511||738||7511||3,(0,0,3) |- | A_E_S_V.gaa.ctg.fa.fas||976||2||2793866||2841116||4||888||890||89||89||0||823||636||77741||2.7363||13539||0.4846||0||88||1||2||170||2481||7758||1589||100||32731||7796||2349||736||7511||738||7511||2,(0,0,2) |- | A_V_S_E.gaa.ctg.fa.fas||977||2||2794330||2841116||4||885||887||92||92||0||819||630||78173||2.7515||13490||0.4828||0||92||1||2||169||2482||7758||1589||100||32731||7796||2349||736||7511||738||7511||2,(0,0,2) |- | E_S_V_A.gaa.ctg.fa.fas||994||2||2790781||2841116||4||903||905||25||25||0||793||633||79673||2.8043||13538||0.4851||0||92||1||1||182||2469||6830||1641||100||37109||6936||2322||765||6803||766||6803||2,(0,0,2) |- | E_V_S_A.gaa.ctg.fa.fas||998||2||2791239||2841116||4||904||906||26||26||0||792||635||79601||2.8018||13538||0.485||0||95||1||1||182||2469||6830||1640||100||37109||6936||2322||766||6803||767||6803||2,(0,0,2) |- | S_V_A_E.gaa.ctg.fa.fas||960||2||2792927||2841116||10||903||905||44||44||0||844||641||75956||2.6735||14757||0.5284||0||61||1||4||171||2480||6398||1616||100||26969||6440||2351||780||6360||781||6355||3,(0,0,3) |- | V_E_S_A.gaa.ctg.fa.fas||1201||2||2798344||2841116||4||1104||1106||58||58||0||998||835||79219||2.7883||17817||0.6367||0||98||1||1||225||2426||5329||1319||100||22892||5335||2248||943||5322||945||5322||2,(0,0,2) |- | V_E_A_S.gaa.ctg.fa.fas||1202||2||2798250||2841116||4||1098||1100||55||55||0||992||829||80446||2.8315||17694||0.6323||0||105||1||1||224||2427||5329||1319||100||22892||5335||2248||941||5322||943||5322||2,(0,0,2) |- | V_A_S_E.gaa.ctg.fa.fas||1203||2||2798480||2841116||4||1104||1106||134||134||0||996||830||79769||2.8077||17762||0.6347||0||100||1||1||224||2427||5329||1319||100||22892||5335||2248||941||5322||943||5322||2,(0,0,2) |- | |} [^] Please note that the ContigN50 calculated by Mauve Assembly Metrics is incorrect (off-by-one error). We have followed the definition of N50 (''A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list.'' [http://www.ncbi.nlm.nih.gov/pubmed/22510764 ref]) to calculate N50s. GAGE's N50 was calculated using the total reference genome length rather than the sum total of contig lengths. The GAGE's cor.N50 values were computed after correcting contigs by breaking them at each error.