Difference between revisions of "Francisella tularensis holarctica KO97"

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'''2007_0907_AMOScmp-454-OSU18'''
 
'''2007_0907_AMOScmp-454-OSU18'''
   22 contigs, 1,895,602 bp
+
   22 contigs, 1,895,404 bp

Revision as of 15:34, 26 November 2007

Center: Baylor

 Status: Assembly (126 contigs; 1,763,979 bp; maxLen=77,480 bp; avgLen=13,999 bp)

Data

Libraries:

 CENTER  PROJECT     STRAIN   LIB               TYPE SIZE STDEV COUNT   LOCATION
 BCM     BFTH        KO97     BFTHP             WGS 6,250 1,250 1,439   TA
 BCM     BFTG        KO97     BFTGP             WGS 4,000 1,000 1,469   TA
 BCM     4WG_FTUL.KO KO971026 4WG_FTUL.KO_000pA 454 .     .     212,588 SRA ?
 BCM     4WG_FTUL.KO KO971026 4WG_FTUL.KO_000sA 454 .     .     431,608 SRA
 Total                                                          647,104

Assembly

Location:

 /fs/szasmg2/Bacteria/F_tularensis_holarctica_KO97

2007_0821_454

 newbler assembly of 4WG_FTUL.KO_000sA library
 => 123 LargeContigs, 1,760,154 bp
 /*
 **  Consensus results.
 */
 consensusResults
 {
       readStatus
       {
               numberAssembled = 399279;
               numberPartial   = 8579;
               numberSingleton = 5027;
               numberRepeat    = 17452;
               numberOutlier   = 1271;
       }

       largeContigMetrics
       {
               numberOfContigs   = 123;
               numberOfBases     = 1760154;

               avgContigSize     = 14310;
               N50ContigSize     = 21671;
               largestContigSize = 52092;

               Q40PlusBases      = 1755769, 99.75%;
               Q39MinusBases     = 4385, 0.25%;
       }

       allContigMetrics
       {
               numberOfContigs = 175;
               numberOfBases   = 1767552;
       }
 }

2007_0822_454

 newbler assembly of 4WG_FTUL.KO_000p & 4WG_FTUL.KO_000sA libraries
 => 12 Scaffolds, 114 LargeContigs, 1,751,786 bp; gap sizes are not "estimated"
 /*
 **  Consensus results.
 */
 consensusResults
 {
       readStatus
       {
               numberAssembled = 399206;
               numberPartial   = 8743;
               numberSingleton = 5027;
               numberRepeat    = 17277;
               numberOutlier   = 1355;
       }

       pairedReadStatus
       {
               numberWithBothMapped   = 160501;
               numberWithOneUnmapped  = 6487;
               numberMultiplyMapped   = 16987;
               numberWithBothUnmapped = 354;
       }

       scaffoldMetrics
       {
               numberOfScaffolds   = 12;
               numberOfBases       = 1761805;

               avgScaffoldSize     = 146817;
               N50ScaffoldSize     = 307646;
               largestScaffoldSize = 341670;
       }

       largeContigMetrics
       {
               numberOfContigs   = 114;
               numberOfBases     = 1751786;

               avgContigSize     = 15366;
               N50ContigSize     = 21680;
               largestContigSize = 52088;

               Q40PlusBases      = 1747448, 99.75%;
               Q39MinusBases     = 4338, 0.25%;
       }

       allContigMetrics
       {
               numberOfContigs = 174;
               numberOfBases   = 1767690;
       }
 }
NC_008369-K097.png OSU18 vs K097 newbler scaffolds
F_tularensis_holarctica_KO97.de_novo.454Scaffolds-454Scaffolds.png 454Scaffolds vs 454Scaffolds

2007_0829_AMOScmp_454-OSU18 -> best

 AMOScmp with default parameters
 ref: OSU18
 => 1 scaff, 101 contigs, 1894065 bp

2007_0831_454

 454 mapping assembly
 ref: OSU18
 /*
 **  Consensus results.
 */
 consensusResults
 {
       readStatus
       {
               numberFullyMapped     = 379431, 58.90%;
               numberPartiallyMapped = 17146, 2.66%;
               numberUnmapped        = 212572, 33.00%;
               numberRepeat          = 35047, 5.44%;
       }
       largeContigMetrics
       {
               numberOfContigs   = 107;
               numberOfBases     = 1745863;
               avgContigSize     = 16316;
               N50ContigSize     = 23834;
               largestContigSize = 87521;
               Q40PlusBases      = 1740564, 99.70%;
               Q39MinusBases     = 5299, 0.30%;
               numUndercalls     = 1217;
               numOvercalls      = 864;
               numHCUndercalls   = 851;
               numHCOvercalls    = 700;
               consensusAccuracy  = 99.8808%;
               HCconsensusAccuracy  = 99.9109%;
       }
       allContigMetrics
       {
               numberOfContigs = 137;
               numberOfBases   = 1749536;
       }
 }

2007_0907_AMOScmp-454-OSU18

 22 contigs, 1,895,404 bp