Francisella tularensis

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


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 .


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

http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=francisella%20tularensis

ftp://@ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/BCM/

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&size=310747&val=species_code=%22Francisella+tularensis%22+&file=trace&gz=on&fasta=on&dopt=fasta&dispmax=5&page=1

ftp://@ftp.ncbi.nih.gov/pub/TraceDB/francisella_tularensis

http://www.broad.mit.edu/seq/msc/

http://www.broad.mit.edu/annotation/genome/francisella_tularensis_group/MultiDownloads.html

http://www.hgsc.bcm.tmc.edu/projects/microbial/microbial-index.xsp

ftp://@ftp.hgsc.bcm.tmc.edu/pub/data/


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 .


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

http://sourceforge.net/projects/wgs-assembler/

http://sourceforge.net/projects/AMOS

http://www.454.com/enabling-technology/the-software.asp


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


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%


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)


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

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


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


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


Mummerplot: OSU18 vs OSU18; red lines beside the main diagonal are repeats


Mummerplot: OSU18(Type B) vs SchuS4(Type A); many rearrangements


Mummerplot: OSU18(Type B) vs U112(Novicida); many rearrangements


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


Mummerplot: OSU18 (complete) vs OSU18 (WGA): 2 inversions & several indels


Mummerplot: OSU18 (complete) vs OSU18 (WGA): SNP's are represented as red dots


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


Hawkeye: Original AMOcmp assembly; many orientation violations (red mates) indicate missassemblies


Hawkeye: Original AMOcmp assembly: 1st missassembled region

16,336-21,562 (5 KB)


Hawkeye: Original AMOcmp assembly: 2nd missassembled region

167,086-184,936 (17 KB)


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.


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


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

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=148928511


Mummerplot: SchuS4(Type A, complete) vs FSC033(Type A,draft)


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


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



Size 4,500 4,500 4,500 4,500 .

Stdev 450 450 450 450 .

#Traces 768 768 768 768 553,908


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



Size 4,500 4,500 4,500 4,500 .

Stdev 450 450 450 450 .

#Traces 768 768 19,968 768 233,823


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

Documents

Francisella tularensis