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Source database (GenBank or RefSeq) File type

allMis0.2

This assembly has been replaced. See current version

Organism name:

Alligator mississippiensis (American alligator)

BioSample:

SAMN02981418

BioProject:

PRJNA159843

Submitter:

International Crocodilian Genomes Working Group

Date:

2012/07/24

Synonyms:

allMis1

Assembly level:

Scaffold

Genome representation:

full

GenBank assembly accession:

GCA_000281125.1 (replaced)

RefSeq assembly accession:

GCF_000281125.1 (suppressed) see latest RefSeq assembly for this species

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome MT

Data displayed for GenBank version

WGS Project:

AKHW01

Assembly method:

Allpaths v. R41313; manual scaffolding

Genome coverage:

68x

Sequencing technology:

Illumina

IDs: 406428 [UID] 406428 [GenBank] 864148 [RefSeq]

See Genome Information for Alligator mississippiensis

Pathogen Detection Resources

There are 5 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_000281125.4	≠	GCF_000281125.3	ASM28112v4	Scaffold	Latest GenBank, RefSeq suppressed
GCA_000281125.3	≠	GCF_000281125.2	ASM28112v3	Scaffold	Replaced GenBank, RefSeq suppressed
GCA_000281125.2	n/a	n/a	ASM28112v2	Scaffold	GenBank suppressed
GCA_000281125.1	≠	GCF_000281125.1	allMis0.2	Scaffold	Replaced GenBank, RefSeq suppressed

Comment

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.

Global statistics

Total sequence length	2,174,243,242
Total ungapped length	2,129,643,287
Gaps between scaffolds	0
Number of scaffolds	14,644
Scaffold N50	508,966
Scaffold L50	1,206
Number of contigs	114,158
Contig N50	36,484
Contig L50	17,211
Total number of chromosomes and plasmids	0
Number of component sequences (WGS or clone)	114,158

Assembly

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allMis0.2

See Genome Information for Alligator mississippiensis

Pathogen Detection Resources

There are 5 assemblies for this organism

History (Show revision history)

Comment

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