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allMis0.2

Organism name:
Alligator mississippiensis (American alligator)
BioSample:
SAMN02981418
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 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT.
  • Data displayed for RefSeq 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

There are 3 assemblies for this organism

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History (Show revision history)

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 length2,174,259,888
Total assembly gap length44,599,955
Gaps between scaffolds0
Number of scaffolds14,645
Scaffold N50508,966
Scaffold L501,206
Number of contigs114,159
Contig N5036,484
Contig L5017,211
Total number of chromosomes and plasmids1

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
non-nuclear
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced2,174,243,24214,6442,129,643,287508,96699,5140
MoleculeTotal
Length
Mitochondrion MT16,646