francisella tularensis. data sources ncbi ● genome projects genome projects ● short read archive...
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Francisella tularensis
CharacteristicsGamma—proteobacteriumIntracellular pathogenOne of the most infectious human pathogensCausative agent of tularemiaCategory A biodefense concern : ability to cause incapacitating, potentially fatal illness
Subspecies Virulence StrainsTularensis (Type A) high ATCC6223, FSC033, FSC198, SchuS4, WY96-3418Holarctica (Type B) moderate 257, FSC022, FSC200, FTA, K097, LSV, MI001730, OR960246, OUS18, RC503, URTF1Novicida moderate GA99-3548, GA99-3549, U112Mediasiatica low FSC147
Status StrainsComplete Schu S4, FSC198, WY96-3418, LSV, OSU18, U112Assembly FSC033,ATCC6223, KO97, MI001730, OR960246, RC503, 275, FSC022,FSC200, GA99-3548, GA99-3549Progress FTA, URFT1, FSC147
Francisella tularensis
Genome Centers #Strains Trace Availability
BioHealthBase 2 NoBroad Institute 5 Yes
Baylor College of Medicine 6 YesDOE Joint Genome Institute 1 No
LLNL/ORNL 1 No
Swedish Defence Research Agency 1 NoUniv. of Birmingham 1 NoUniv. of Washington 2 NoUnite des Ricketts ies 1 No
Total 20 .
Francisella tularensis
Data Sources
NCBI
● Genome Projects● Short Read Archive (SRA)● Trace Archive (TA)● TA FTP
Broad Institute
● Microbial Sequencing Center● Download Sequence
Baylor College of Medicine
● Microbial Genome Projects● FTP
Francisella tularensis
DATA SUMMARYSubspecies Strain Center Status #Contigs Length #Sanger #454 #Traces NcbiRefType A ATCC6223 Baylor Assembly 88 1,757,628 2,144 627,012 629,156 .
Type A FSC033 Broad Assembly 15 1,844,205 23,040 278,235 301,275 NZ_AAYE00000000Type A FSC198 Univ. of Birmingham Complete 1 1,892,616 0 0 0 NC_008245Type A Schu S4 SDRA Complete 1 1,892,819 0 0 0 NC_006570Type A WY96-3418 BioHealthBase Complete 1 1,898,476 0 0 0 NC_009257
Type B 275 Broad Assembly 31 1,886,241 29,952 901,724 931,676 NZ_AAUD00000000Type B FSC022 Broad Assembly 19 1,858,527 3,072 553,908 556,980 NZ_AAYD00000000Type B FSC200 Univ of Washington Assembly 39 1,790,358 0 0 0 NZ_AASP00000000Type B FTA BioHealthBase Progress . . 0 0 0 .Type B K097 Baylor Assembly 126 1,763,979 2,908 644,196 647,104 .Type B LSV LLNL Complete 1 1,895,994 0 0 0 NC_007880Type B MI001730 Baylor Assembly 118 1,765,520 0 746,772 746,772 .Type B OR960246 Baylor Assembly 111 1,761,162 0 621,681 621,681 .Type B OSU18 Baylor Complete 1 1,895,727 68,462 527,242 595,704 NC_008369Type B RC503 Baylor Assembly 115 1,760,469 0 687,860 687,860 .Type B URTF1 Unite des Rickettsies Progress . . 0 0 0 .
Novicida GA99-3548 Broad Assembly 18 1,845,491 24,576 17,731 42,307 NZ_ABAH00000000Novicida GA99-3549 Broad Assembly 15 1,897,440 22,272 233,823 256,095 NZ_AAYF00000000Novicida U112 Univ of Washington Complete 1 1,910,03 0 0 0 NC_008601
Mediasitica FSC147 DOE Progress . . 0 0 0 .
Francisella tularensis
Assembly methods:● Whole Genome Assembly (WGA): Celera
● July 18th 2007 version● runCA-OBT.pl script● Sanger traces
● Comparative Assembly : AMOS● 2.0.2 version● AMOScmp script● Sanger/454 traces
● 454● 1.1.01.20 version● runProject script● 454 traces
Francisella tularensis
Whole Genome Assembly● De novo assembly● Does not use a reference genome● Requires high quality long Sanger paired reads● Cannot handle 454 data (yet)● Max error rate=1.5%● Overlap based trimming of the reads● Re-estimate library insert size (mean,stdev)● Resolves surrogates● Creates contigs & scaffolds
Francisella tularensis
AMOScmp● Comparative assembly● Uses a reference genome● Can assemble low quality/short reads● Rearrangements/indels can create breaks in the
assembly● Can use both Sanger & 454 unpaired reads● Max error rate=20%
Francisella tularensis
454 de novo assembler● Does not use a reference genome● Uses 454 unpaired/pair-end reads● Requires 454 flowgrams● Creates contigs ● Creates scaffolds (if pair-end reads are available)
Francisella tularensis
Software used:● Assemblers: WGA, AMOScmp, 454● Data download: ftp, wget, query_tracedb● Data formatting: tarchive2ca(AMOS),sfftools● Trimming: Lucy, veraTrim, OBT● Alignment, repeats, snp's: mummer● Sequence manipulation: EMBOSS● Assembly validation: cavalidate,
amosvalidate(AMOS)● Contig joining: autoJoiner● Scripts: Perl● Wiki site: keep track of the assemblies progress https://wiki.umiacs.umd.edu/cbcb/index.php/Francisella_tularensis
Francisella tularensis holarctica OSU18
The only complete genome for which we have most of the traces available!
Published: Chromosome Rearrangement and Diversification of Francisella tularensis Revealed by the Type B (OSU18) Genome Sequence; J Bacteriol. 2006 October; 188(19): 6977–6985.
Sequencing and assembly of the F. tularensis subsp. holarctica strain OSU18 genome were accomplished by the whole-genome shotgun (WGS) method, similar to a previously described method (22). Briefly, the WGS clones were sequenced using ABI 3730 sequencers, and the sequence bases were called using the Applied Biosystems sequencing analysis software KB Basecaller. The WGS reads were assembled by using Atlas (11) and Phrap (7). The initial WGS assembly resulted in 132 contigs in 33 scaffolds with approximately 26× sequence coverage. Gaps between contigs and scaffolds were closed by sequencing PCR products that spanned gaps or by sequencing small insert libraries generated from the PCR products. Low-quality regions were resequenced using clones or PCR products spanning the regions to ensure that the Phrap quality score for each base was equal to or greater than 30. This relatively deep data set should enable further studies involving new sequencing, comparative genomics, and proteomics strategies and technologies
Francisella tularensis holarctica OSU18Center: Baylor
Status: Complete
INPUT DATA
Seq_lib_id BFTBP BFTDP OS_000sA OS_000pA
Type WGS WGS 454 454
Size 2,000 2,000 . .
Stdev 1,000 1,000 . .
#Traces 58,053 10,409 310,747 216,495
Location TA TA TA SRA
REFERENCE
#Contigs 1
Length 1,895,727
NcbiRef NC_008369
ASSEMBLY
Assembler Celera AMOScmp AMOScmp AMOScmp AMOScmp AMOScmp AMOScmp AMOScmp
Reference . OSU18 OSU18 OSU18 OSU18 OSU18 OSU18 OSU18
Trimming OBT Factory Lucy Lucy+veraTrim veraTrim veraTrim OBT veraTrim
Sanger Yes Yes Yes Yes Yes Yes Yes Yes
454 No No No No No No No No
#Scaff 160 1 1 1 1 1 1 1
#Contigs 163 22 25 17 16 12 11 8
#Bases 2,104,125 1,882,156 1,880,261 1,886,820 1,891,049 1,890,614 1,889,596 1,889,817
MaxScaff 454,878 1,882,156 1,880,261 1,886,820 1,891,049 1,890,614 1,889,596 1,889,817
MeanScaff 13,151 1,882,156 1,880,261 1,886,820 1,891,049 1,890,614 1,889,596 1,889,817
MaxContig 454,878 567,200 454,753 569,031 570,211 573,152 811,544 642,346
MeanContig 12,909 87,546 75,389 113,771 121,419 162,635 173,377 243,858
#Reads 67,220 68,460 68,460 68,460 68,460 68,460 68,460 68,460
#Singletons 2,768 1,989 2,768 3,646 3,341 1,485 2,691 1,492
Comment
. . . . . libInsert updatelibInsert update, AMOScmp relaxed
libInsert update, AMOScmp relaxed, fixed reference
Francisella tularensis holarctica OSU18
Alignments● OSU18 vs OSU18 (complete genome)
● many ~1KB dispersed repeats● one 30KB two copy repeat
● OSU18 vs other strains (SchuS4,U112) (complete genomes)● large rearrangements● indels● SNP's● common repeats
● OSU18 (complete genome) vs OSU18 (assemblies) ● assembly gaps● errors
● OSU18 (complete genome) vs OSU18 (traces) ● read coverage: 4 regions with 0X coverage● trimming● library insert sizes: original values (2KB) are underestimates
Francisella tularensis holarctica OSU18
Trimming● Default (Factory): CLIP values from NCBI TA● Lucy: quality trimming● veraTrimming: 5' vector trimming● Overlap Based Trimming (OBT): quality & vector trimming
method #traces min median max sum mean stdev n50 comment
Default 68,460 9 805 1,139 51,318,158 750 205 827
veraTrim 68,460 -40 836 1,140 53,513,005 782 187 853Lucy 68,460 0 697 1,102 43,612,002 637 226 732 most stringent
lucy & veraTrim 68,460 -42 792 1,099 50,492,970 738 193 812
OBT 68,460 9 838 1,183 53,420,098 780 204 860
Francisella tularensis holarctica OSU18
Mummerplot: OSU18 vs OSU18; red lines beside the main diagonal are repeats
Francisella tularensis holarctica OSU18
Mummerplot: OSU18(Type B) vs SchuS4(Type A); many rearrangements
Francisella tularensis holarctica OSU18
Mummerplot: OSU18(Type B) vs U112(Novicida); many rearrangements
Francisella tularensis holarctica OSU18
WGA metrics:
[Scaffolds]TotalScaffolds=160TotalContigsInScaffolds=163TotalBasesInScaffolds=2104125MeanBasesInScaffolds=13151MinBasesInScaffolds=1028MaxBasesInScaffolds=454878
[Contigs]TotalContigsInScaffolds=163TotalBasesInScaffolds=2104125MeanContigLength=12909MinContigLength=1028MaxContigLength=454878
[BigContigs_greater_10000]TotalBigContigs=19BigContigLength=1869172MeanBigContigLength=98377MinBigContig=13002MaxBigContig=454878BigContigsPercentBases=88.83...
[Mates]ReadsWithNoMate=3052(4.54%)ReadsWithGoodMate=54516(81.10%)ReadsWithBadShortMate=0(0.00%)ReadsWithBadLongMate=26(0.04%)ReadsWithSameOrientMate=122(0.18%)ReadsWithOuttieMate=42(0.06%)ReadsWithBothChaffMate=1744(2.59%)ReadsWithChaffMate=1034(1.54%)
[Reads]TotalUsableReads=67220AvgClearRange=791ContigReads=61480(91.46%)BigContigReads=60524(90.04%)SmallContigReads=956(1.42%)SingletonReads=2768(4.12%)ChaffReads=2768(4.12%)
[Coverage]ContigsOnly=23.31AllReads=25.29
Francisella tularensis holarctica OSU18
Mummerplot: OSU18 (complete) vs OSU18 (WGA): 2 inversions & several indels
Francisella tularensis holarctica OSU18
Mummerplot: OSU18 (complete) vs OSU18 (WGA): SNP's are represented as red dots
Francisella tularensis holarctica OSU18
AMOScmp metrics:
[Scaffolds]TotalScaffolds 1TotalContigsInScaffolds 22MeanContigsPerScaffold 22.00MinContigsPerScaffold 22MaxContigsPerScaffold 22TotalBasesInScaffolds 1882156MeanBasesInScaffolds 1882156MaxBasesInScaffolds 1882156N50ScaffoldBases 1882156TotalSpanOfScaffolds 1895684MeanSpanOfScaffolds 1895684MinScaffoldSpan 1895684MaxScaffoldSpan 1895684IntraScaffoldGaps 21MeanSequenceGapSize 613.91...
[Contigs]TotalContigs 22TotalBasesInContigs 1926006MeanContigSize 87545.73MinContigSize 99MaxContigSize 567200N50ContigBases 465176
...
[BigContigs_greater_10000]TotalBigContigs 10BigContigLength 1918334MeanBigContigSize 191833.40MinBigContig 10681MaxBigContig 567200BigContigsPercentBases 99.60
[SmallContigs]TotalSmallContigs 12SmallContigLength 7672MeanSmallContigSize 639.33MinSmallContig 99MaxSmallContig 2153SmallContigsPercentBases 0.40
[Reads]TotalReads 68460ReadsInContigs 66471BigContigReads 66367SmallContigReads 104SingletonReads 1989
Francisella tularensis holarctica OSU18
Hawkeye: Original AMOcmp assembly; many orientation violations (red mates) indicate missassemblies
Francisella tularensis holarctica OSU18
Hawkeye: Original AMOcmp assembly: 1st missassembled region
16,336-21,562 (5 KB)
Francisella tularensis holarctica OSU18
Hawkeye: Original AMOcmp assembly: 2nd missassembled region
167,086-184,936 (17 KB)
Francisella tularensis holarctica OSU18
Final Assembly Steps:
1. The complete genome sequence was downloaded from NCBI: RefSeq NC_008369.12. The reads were downloaded from TA and re-formatted using the AMOS package (tarchive2ca)
=> .frg & .afg files3. Only the two Sanger libraries were considered: 68K reads should provide enough coverage to
assemble the whole genome4. The reads were retrimmed using veraTrim (-T 10 -M 100 -E 500)5. The WGA assembler (runCA-OBT.pl) was used to assemble the reads 6. The library sizes were updated using the WGA estimates BFTBP (mean,stdev): original (2000,1000) ; WGA (2690, 643) BFTDP (mean,stdev): original (2000,1000) ; WGA (3675,1225)7. The WGA assembly was aligned to the reference using nucmer; two rearrangements & multiple
SNP's were noticed8. The reads were assembled using AMOScmp; 2 missoriented read piles were noticed9. The assembly was aligned to itself; two 950 bp inverted repeats were identified as flanking the
problem regions; the region coordinates are: 16336-21562 (5 KB), 167086-184936 (17 KB)10. The 2 regions were flipped ; the new reference was called NC_008369.211. Several small contig read clear ranges (step 8) were extended to their OBT trimming points12. AMOScmp was rerun using more relaxed parameters: nucmer MINCLUSTER=30 , casm-layout MAXTRIM=50
Conclusions:
We Reduced the number of AMOScmp contigs from 22 to 8.We increased the number of assembled bases from 1,882,156 to 1,889,817.
Francisella tularensis holarctica OSU18
New AMOcmp assembly: the 2 piles of orientation violations (red mates) are gone
Francisella tularensis tularensis FSC033
Center: Broad
Status: Draft
INPUT DATA
Seq_lib_id G907A1 G907A2 G907A3 G907A4 454-410
Type WGS WGS WGS WGS 454
Size 4,500 4,500 4,500 4,500 .
Stdev 450 450 450 450 .
#Traces 768 768 20,736 768 278,235
Location TA TA TA TA TA
REFERENCE
#Contigs 15
Length 1,844,205
NcbiRef NZ_AAYE00000000
ASSEMBLY
Assembler Celera AMOScmp AMOScmp AMOScmp AMOScmp AMOScmp
Reference . FSC033 FSC033 FSC033 SchuS4 SchuS4
Trimming OBT Factory OBT OBT OBT OBT
Sanger Yes Yes Yes Yes Yes Yes
454 No No No Yes Yes No
#Scaff 12 13 13 15 1 1
#Contigs 23 32 23 20 10 26
#Bases 1,882,120 1,830,876 1,834,381 1,844,360 1,893,035 1,873,341
MaxScaff 392,624 644,953 647,962 650,327 1,893,035 1,873,341
MeanScaff 156,843 140,837 141,106 122,957 1,893,035 1,873,341
MaxContig 388,104 270,451 395,944 626,237 625,816 386,995
MeanContig 81,831 58,799 80,263 100,489 206,120 72,501
#Reads 22,207 22,713 22,713 300,948 300,948 22,713
#Singletons 22 1,946 563 10,187 7,005 501
Francisella tularensis tularensis FSC033
Reference: NZ_AAYE00000000
Name Length %GCNZ_AAYE01000001.1 101124 33.65NZ_AAYE01000002.1 46675 32.87NZ_AAYE01000003.1 1600 34.25NZ_AAYE01000004.1 295522 31.87NZ_AAYE01000005.1 650364 31.73NZ_AAYE01000006.1 2400 37.29NZ_AAYE01000007.1 132212 32.96NZ_AAYE01000008.1 23680 31.04NZ_AAYE01000009.1 201 45.27 high GC%: 16S-23S
rRNA(megablast)NZ_AAYE01000010.1 571 46.06 high GC%NZ_AAYE01000011.1 61231 32.30NZ_AAYE01000012.1 249955 31.91NZ_AAYE01000013.1 137017 32.24NZ_AAYE01000014.1 91009 32.87NZ_AAYE01000015.1 50644 33.42Total 1844205
1,892,819 bp in SCHU S4(complete)=> ~ 48,614 bp FSC033 draft assembly gaps
Francisella tularensis tularensis FSC033
Mummerplot: SchuS4(Type A, complete) vs FSC033(Type A,draft)
Francisella tularensis tularensis FSC033
AMOScmp assembly, Sanger+454 reads, FSC033 Broad draft assembly used as reference
3rd largest scaffold: 30 KB repeat looks collapsed; appears as 28,659 bp surrogate in WGA
Francisella tularensis tularensis FSC033
AMOScmp assembly, Sanger+454 reads, SchuS4 complete genome used as reference
Francisella tularensis tularensis ATCC6223Center: Baylor
Status: Draft
INPUT DATA
Seq_lib_id BFTFP AT_000SA AT_000pA
Type WGS 454 454
Size 6,250 . .
Stdev 1,250 . .
#Traces 2,144 408,780 218,232
Location TA TA SRA
REFERENCE
#Contigs 88
Length 1,757,628
NcbiRef .
ASSEMBLY
Assembler AMOScmp AMOScmp AMOScmp AMOScmp
Reference ATCC6223 FSC198 SchuS4 WY96-3418
Trimming Factory Factory Factory Factory
Sanger Yes Yes Yes Yes
454 Yes Yes Yes Yes
#Scaff 88 1 1 1
#Contigs 188 195 194 144
#Bases 1,762,423 1,761,838 1,759,427 1,766,012
MaxScaff 133,922 1,761,838 1,759,427 1,766,012
MeanScaff 20,028 1,761,838 1,759,427 1,766,012
MaxContig 77,626 68,138 68,138 78,138
MeanContig 10,364 9,939 9,978 13,529
#Reads 410,924 410,924 410,924 410,924
#Singletons 54,290 71,958 71,964 66,782
Francisella tularensis holarctica 257
Center: Broad
Status: Draft
INPUT DATA
Seq_lib_id G878A2 G878A1 G878A9 G878A5 G878A4 G878A3 G878A10 G878A12 G878A11 454-255
Type WGS WGS WGS WGS WGS WGS WGS WGS WGS 454
Size 4,500 4,500 10,000 4,500 4,500 4,500 10,000 10,000 10,000 .
Stdev 450 450 1,000 450 450 450 1,000 1,000 1,000 .
#Traces 768 23,808 768 768 768 768 768 768 768 901,724
Location TA TA TA TA TA TA TA TA TA TA
REFERENCE
#Contigs 31
Length 1,886,241
NcbiRef NZ_AAUD00000000
ASSEMBLY
Assembler Celera AMOScmp
Reference . 257
Trimming OBT OBT
Sanger Yes Yes
454 No Yes
#Scaff 10 26
#Contigs 33 45
#Bases 1,861,251 1,848,389
MaxScaff 558,083 270,354
MeanScaff 186,125 71,091
MaxContig 327,202 322,011
MeanContig 56,402 50,035
#Reads 27,116 931,121
#Singletons 187 181,694
Francisella tularensis holarctica FSC022Center: Broad
Status: Draft
INPUT DATA
Seq_lib_id G790A5 G790A6 G790A7 G790A8 454-411
Type WGS WGS WGS WGS 454
Size 4,500 4,500 4,500 4,500 .
Stdev 450 450 450 450 .
#Traces 768 768 768 768 553,908
Location TA TA TA TA TA
REFERENCE
#Contigs 19
Length 1,858,527
NcbiRef NZ_AAYD00000000
ASSEMBLY
Assembler AMOScmp
Reference FSC022
Trimming Factory
Sanger Yes
454 Yes
#Scaff 16
#Contigs 71
#Bases 1,823,163
MaxScaff 503,439
MeanScaff 113,948
MaxContig 208,201
MeanContig 28,003
#Reads 556,946
Francisella tularensis holarctica KO97Center: Baylor
Status: Draft
INPUT DATA
Seq_lib_id BFTHP BFTGP KO_000pA KO_000sA
Type WGS WGS 454 454
Size 6,250 4,000 . .
Stdev 1,250 1,000 . .
#Traces 1,439 1,469 212,588 431,608
Location TA TA SRA SRA
REFERENCE
#Contigs 126
Length 1,763,979
NcbiRef .
ASSEMBLY
Assembler Newbler Newbler AMOScmp
Reference . . OSU18
Trimming Factory Factory Factory
Sanger No No No
454 Yes(unpaired) Yes(unpaired,pair-end) Yes(unpaired)
#Scaff 123 12 1
#Contigs 175 174 101
#Bases 1,767,552 1,767,690 1,894,065
MaxScaff 52,092 341,670 1,894,065
MeanScaff 14,310 146,817 1,894,065
MaxContig 52,092 52,088 117,151
MeanContig 14,310 15,366 20,614
#Reads 431,608 431,608 431,608
#Singletons 5,027 5,027 64,527
Francisella tularensis holarctica KO97
AMOScmp assembly, 454 unpaired reads, OSU18 complete genome used as reference
Francisella tularensis holarctica MI001730Center: Baylor
Status: Draft
INPUT DATA
Seq_lib_id MI_000pA MI_000sA
Type 454 454
Size . .
Stdev . .
#Traces 162,763 584,009
Location SRA SRA
REFERENCE
#Contigs 126
Length 1,763,979
NcbiRef .
ASSEMBLY
Assembler Newbler
Reference .
Trimming Factory
Sanger No
454 Yes
#Scaff 15
#Contigs 177
#Bases 1,771,992
MaxScaff 364,856
MeanScaff 117,293
MaxContig 87,351
MeanContig 18,058
#Reads 584,009
#Singletons 3,066
Francisella tularensis holarctica OR960246Center: Baylor
Status: Draft
INPUT DATA
Seq_lib_id OR_000sA OR_000pA
Type 454 454
Size . .
Stdev . .
#Traces 401,300 220,381
Location SRA SRA
REFERENCE
#Contigs 111
Length 1,761,162
NcbiRef .
ASSEMBLY
Assembler Newbler
Reference .
Trimming Factory
Sanger No
454 Yes
#Scaff 13
#Contigs 224
#Bases 1,776,919
MaxScaff 787,808
MeanScaff 135,663
MaxContig 75,931
MeanContig 16,246
#Reads 401,300
#Singletons 5,966
Francisella tularensis holarctica RC503Center: Baylor
Status: Draft
INPUT DATA
Seq_lib_id RC_000SA RC_000pA
Type 454 454
Size . .
Stdev . .
#Traces 498,744 189,116
Location TA SRA
REFERENCE
#Contigs 115
Length 1,760,469
NcbiRef .
ASSEMBLY
None
Francisella tularensis novicida GA99-3548Center: Broad
Status: Draft
INPUT DATA
Seq_lib_id G909A2 G909A4 G909A3 454-414
Type WGS WGS WGS 454
Size 4,500 4,500 4,500 .
Stdev 450 450 450 .
#Traces 768 768 23,040 17,731
Location TA TA TA TA
REFERENCE
#Contigs 18
Length 1,845,491
NcbiRef NZ_ABAH00000000
ASSEMBLY
Assembler Celera AMOScmp AMOScmp
Reference . GA99-3548 GA99-3548
Trimming OBT Factory OBT
Sanger Yes Yes Yes
454 No No Yes
#Scaff 8 11 13
#Contigs 18 24 35
#Bases 1,839,522 1,830,675 1,839,125
MaxScaff 449,792 622,987 622,985
MeanScaff 229,940 166,425 141,471
MaxContig 377,748 333,175 328,180
MeanContig 102,196 78,298 53,177
#Reads 22,543 23,721 41,452
#Singletons 59 2,189 3,941
Francisella tularensis novicida GA99-3549Center: Broad
Status: Draft
INPUT DATA
Seq_lib_id G908A2 G908A4 G908A1 G908A3 454-413
Type WGS WGS WGS WGS 454
Size 4,500 4,500 4,500 4,500 .
Stdev 450 450 450 450 .
#Traces 768 768 19,968 768 233,823
Location TA TA TA TA TA
REFERENCE
#Contigs 15
Length 1,897,440
NcbiRef NZ_AAYF00000000
ASSEMBLY
Assembler Celera AMOScmp
Reference . GA99-3549
Trimming OBT OBT
Sanger Yes Yes
454 No Yes
#Scaff 9 13
#Contigs 27 15
#Bases 1,897,966 1,895,402
MaxScaff 645,439 610,688
MeanScaff 210,885 145,800
MaxContig 293,026 548,892
MeanContig 70,295 132,343
#Reads 20,654 255,735
#Singletons 25 21,862