Brugia malayi: Difference between revisions
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| Line 31: | Line 31: | ||
good ctg GC% | good ctg GC% | ||
#elem min max mean median n50 | #elem min max mean median n50 | ||
all 26878 0.00 72.30 28.86 28.56 29.46 | all 26878 0.00 72.30 '''28.86''' 28.56 29.46 | ||
10K+ 1224 24.38 38.44 30.38 30.43 30.62 | 10K+ 1224 24.38 38.44 '''30.38''' 30.43 30.62 | ||
contaminant ctg len | contaminant ctg len | ||
#elem min max mean median n50 sum | #elem min max mean median n50 sum | ||
all 2929 200 8994 740 675 763 2167588 | all 2929 200 8994 740 675 763 '''2167588''' | ||
contaminant ctg GC% | contaminant ctg GC% | ||
#elem min max mean median n50 | #elem min max mean median n50 | ||
all 2929 18.09 75.96 44.1 43.59 44.80 | all 2929 18.09 75.96 '''44.1''' 43.59 44.80 | ||
== Traces == | == Traces == | ||
Revision as of 14:21, 19 August 2008
Articles
Genome Info
- 6 chromosomes: 1-5, XY
- ~ 90M, 30% GC, 32% coding, 15% repeats
Other sequences
- mitochondrion finished: 13,657 bp; 24% GC
- Wolbachia endosymbiont strain TRS from Brugia malayi strain wMel complete: 1,080,084 bp; 34%GC (New England Biolabs)
- Wolbachia endosymbiont strain wMel progress (TIGR)
- Rodent: some trace contamination; Example: Mus musculus is ~40%GC
Genome Project
- NCBI Genome project
- TIGR Genome project (TRS strain)
- NCBI AAQA00000000 AAQA01000001-AAQA01029808
* 26,879 good ctgs * 2,929 contaminants (Example: AAQA01001321 : mouse 99%id hits)
good ctg len
#elem min max mean median n50 sum
all 26879 200 611244 3241 1005 19005 87119350
10K+ 1224 10036 611244 41018 23135 60727 50206329
good ctg GC%
#elem min max mean median n50
all 26878 0.00 72.30 28.86 28.56 29.46
10K+ 1224 24.38 38.44 30.38 30.43 30.62
contaminant ctg len
#elem min max mean median n50 sum
all 2929 200 8994 740 675 763 2167588
contaminant ctg GC%
#elem min max mean median n50
all 2929 18.09 75.96 44.1 43.59 44.80
Traces
Libraries: * 2K : bulk of the sequence @TIGR * 15-20 K @TIGR * 8,000 BAC clones @Children's Hospital Oakland Research Institute. (!!! no NCBI TA submission)
Trace summary:
* all: 1,260,215
* TRACE_TYPE_CODE
* WGS: 1,258,277
* TRANSPOSON: 1,437
* PRIMER_WALK 501
* CENTER NAME
* TIGR: 856,624
* JCVI 403,591
* NO BACS !!!; max INSERT_SIZE=23K
Assemblies
TIGR
- 9X coverage, 856K Sanger traces => 8,200 scaff & 29,808 ctg (avg. scaff=~10K & avg ctg=~3K)
- "scaffolds totaling ~71 Mb of data with a further ~17.5 Mb of contigs not integrated into any scaffold (orphan contigs)" (Science 2007)
CBCB
Files
/fs/szattic/asmg1/adelcher/Genomes/Brugia : Art's files /fs/szasmg3/dpuiu/Brugia_malayi/