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AKHW00000000.1 Alligator mississippiensis

This project is replaced

# of Contigs: 114,158 (114158 are dead)
# of Proteins: 0
# of Scaffolds/Chrs: 8,897 (8897 are dead)
Total length: 2,129,643,287 bp
BioProject: PRJNA159843
BioSample: SAMN02981418
Keywords: WGS
Organism: Alligator mississippiensisshow lineagehide lineage
/country = USA: Florida
/mol_type = genomic
/note = assembly comes from two alligators
WGS: AKHW01000001:AKHW01114158
Scaffolds: JH730990:JH739886
8,897 scaffolds, total length is 2,144,153,452 bases
Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes : Genome Biol. 13 (1), 415 (2012) – show 48 authorshide authors
St John,J.A., Braun,E.L., Isberg,S.R., Miles,L.G., Chong,A.Y., Gongora,J., Dalzell,P., Moran,C., Bed'hom,B., Abzhanov,A., Burgess,S.C., Cooksey,A.M., Castoe,T.A., Crawford,N.G., Densmore,L.D., Drew,J.C., Edwards,S.V., Faircloth,B.C., Fujita,M.K., Greenwold,M.J., Hoffmann,F.G., Howard,J.M., Iguchi,T., Janes,D.E., Khan,S.Y., Kohno,S., de Koning,A.J., Lance,S.L., McCarthy,F.M., McCormack,J.E., Merchant,M.E., Peterson,D.G., Pollock,D.D., Pourmand,N., Raney,B.J., Roessler,K.A., Sanford,J.R., Sawyer,R.H., Schmidt,C.J., Triplett,E.W., Tuberville,T.D., Venegas-Anaya,M., Howard,J.T., Jarvis,E.D., Guillette,L.J. Jr., Glenn,T.C., Green,R.E., Ray,D.A.
Submitted (31-MAY-2012) Biomolecular Engineering, University of California Santa Cruz, 1156 High St Mail Stop SOE-Grads, Santa Cruz, CA 95064, USA – St John,J.A., Green,R.E., Braun,E.L., Ray,D.A.

[WARNING] On Oct 30, 2015 this project was updated. The new version is gi:944465989.

The Alligator mississippiensis whole genome shotgun (WGS) project has the project accession AKHW00000000. This version of the project (01) has the accession number AKHW01000000, and consists of sequences AKHW01000001-AKHW01114158.

BAC-end scaffolding was done with BWA v. 0.6.1-r112-master, samtools v. 0.1.18-dev (r982:313), and SGA v. 0.9.19. Assembled transcripts were also used to scaffold the genome with blat v. 34x12, pslReps filtering and SGA v. 0.9.19.

Assembly Method : Allpaths v. R41313; manual scaffolding
Assembly Name : allMis0.2
Long Assembly Name : Alligator mississippiensis 0.2
Genome Coverage : 68x
Sequencing Technology : Illumina
GenBank:AKHW01.1.gbff.gz 215.1 Mb
 AKHW01.2.gbff.gz 215.2 Mb
 AKHW01.3.gbff.gz 215.1 Mb
 AKHW01.4.gbff.gz 215.1 Mb
 AKHW01.5.gbff.gz 59.7 Mb
FASTA:AKHW01.1.fsa_nt.gz 146.3 Mb
 AKHW01.2.fsa_nt.gz 146.3 Mb
 AKHW01.3.fsa_nt.gz 146.3 Mb
 AKHW01.4.fsa_nt.gz 146.3 Mb
 AKHW01.5.fsa_nt.gz 40.6 Mb
ASN.1:AKHW01.1.bbs.gz 134.8 Mb
 AKHW01.2.bbs.gz 134.8 Mb
 AKHW01.3.bbs.gz 134.8 Mb
 AKHW01.4.bbs.gz 134.9 Mb
 AKHW01.5.bbs.gz 37.5 Mb
Minor Version Create Date
1 07/24/2012
4 02/16/2017