Francisella tularensis holarctica KO97: Difference between revisions
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[[Media:NC_008369-K097.png|NC_008369-K097.png]] OSU18 vs K097 newbler scaffolds | [[Media:NC_008369-K097.png|NC_008369-K097.png]] OSU18 vs K097 newbler scaffolds | ||
''' | '''2007_0829_AMOScmp_454-OSU18''' | ||
AMOScmp with default parameters | |||
ref: OSU18 | |||
=> 1 scaff, 101 contigs, 1894065 bp | |||
'''2007_0831_454''' | |||
454 mapping assembly | |||
ref: OSU18 | |||
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; | |||
} | |||
} |
Revision as of 19:31, 31 August 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 -> best
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
2007_0829_AMOScmp_454-OSU18
AMOScmp with default parameters ref: OSU18 => 1 scaff, 101 contigs, 1894065 bp
2007_0831_454
454 mapping assembly ref: OSU18
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; } }