Francisella tularensis tularensis FSC033: Difference between revisions
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lib: G907A3 mean=4274.536 stdev=110.196 (probably underestimate due to low coverage) | lib: G907A3 mean=4274.536 stdev=110.196 (probably underestimate due to low coverage) | ||
=> 12 scaff, 23 contigs | => 12 scaff, 23 contigs, 1,882,120 bp | ||
'''2007_0807_AMOScmp-OBT''' | '''2007_0807_AMOScmp-OBT''' | ||
use read clr, library insert estimates from 2007_0807_WGA | use read clr, library insert estimates from 2007_0807_WGA | ||
=> 13 scaff, 23 contigs | => 13 scaff, 23 contigs, 1,834,339 bp | ||
'''2007_0809_AMOScmp-OBT''' | '''2007_0809_AMOScmp-OBT-454''' | ||
use read clr, library insert estimates from 2007_0807_WGA | use read clr, library insert estimates from 2007_0807_WGA | ||
include the 454 reads | include the 454 reads | ||
=> 15 scaff, | => 15 scaff, 18 contigs, 1,844,162 bp | ||
Revision as of 19:55, 16 August 2007
Center: Broad
Status: Assembly (15 contigs)
Data
Reference:
NZ_AAYE00000000
Name Length %GC NZ_AAYE01000001.1 101124 33.65 NZ_AAYE01000002.1 46675 32.87 NZ_AAYE01000003.1 1600 34.25 NZ_AAYE01000004.1 295522 31.87 NZ_AAYE01000005.1 650364 31.73 NZ_AAYE01000006.1 2400 37.29 NZ_AAYE01000007.1 132212 32.96 NZ_AAYE01000008.1 23680 31.04 NZ_AAYE01000009.1 201 45.27 high GC%: 16S-23S rRNA(megablast) NZ_AAYE01000010.1 571 46.06 high GC% NZ_AAYE01000011.1 61231 32.30 NZ_AAYE01000012.1 249955 31.91 NZ_AAYE01000013.1 137017 32.24 NZ_AAYE01000014.1 91009 32.87 NZ_AAYE01000015.1 50644 33.42 Total 1844205 1,892,819 bp in SCHU S4(complete genome)=> ~ 48,614 bp in gaps
Traces: from NCBI TA
Libraries:
CENTER PROJECT STRAIN LIB TYPE SIZE STDEV COUNT Location WIBR G907 033 G907A1 WGS 4,500 450 768 TA WIBR G907 033 G907A2 WGS 4,500 450 768 TA WIBR G907 033 G907A3 WGS 4,500 450 20,736 TA WIBR G907 033 G907A4 WGS 4,500 450 768 TA WIBR G919 033 454-410 454 . . 278,235 TA StrainSubtotal 301,275
NC_006570-NZ_AAYE00000000.png Mummerplot Francisella tularensis subsp. tularensis Schu 4, complete genome vs Francisella tularensis subsp. tularensis FSC033
Assembly
Locations:
/fs/szasmg/Bacteria/F_tularensis_tularensis_FSC033/
2007_0807_AMOScmp
Uses default trimming AMOScmp => 13 scaff, 32 contigs, 1,830,923 bp
2007_0807_WGA
Only WGS reads runCA-OBT.pl => new read clr, new library insert estimates
clr got shorter by runing OBT (usually is the opposite) . #traces min median max sum mean stdev n50 CLIPPING 22713 1 868 1018 19613029 863.52 68.27 871 OBT 22207 71 785 907 17128190 771.3 75.98 789
lib: G907A3 mean=4274.536 stdev=110.196 (probably underestimate due to low coverage) => 12 scaff, 23 contigs, 1,882,120 bp
2007_0807_AMOScmp-OBT
use read clr, library insert estimates from 2007_0807_WGA => 13 scaff, 23 contigs, 1,834,339 bp
2007_0809_AMOScmp-OBT-454
use read clr, library insert estimates from 2007_0807_WGA include the 454 reads => 15 scaff, 18 contigs, 1,844,162 bp