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idAnoMarsDA_429_01

Organism name:
Anopheles marshallii (mosquitos)
BioSample:
SAMEA12928237
BioProject:
PRJEB53264
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2022/06/24
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_943734725.1 (latest)
RefSeq assembly accession:
GCF_943734725.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
CALSDX01
Genome coverage:
51x
Linked assembly:
GCA_943734855.1 (alternate pseudohaplotype of diploid)

IDs: 13067131 [UID] 34135098 [GenBank] 40782068 [RefSeq]

See Genome Information for Anopheles marshallii

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The assembly idAnoMarsDA_429_01 is based on 51x PacBio HiFi data, 10X Genomics Chromium data, and Arima Hi-C data generated by the Anopheles Reference Genomes project. The assembly process included the following sequence of steps: initial PacBio assembly generation with ... hifiasm, retained haplotig separation with purge_dups, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named, ordered and oriented based on published data.  more

Global statistics

Total sequence length225,727,465
Total ungapped length225,722,465
Gaps between scaffolds0
Number of scaffolds289
Scaffold N5084,416,232
Scaffold L502
Number of contigs305
Contig N5032,607,359
Contig L503
Total number of chromosomes and plasmids4
Number of component sequences (WGS or clone)289

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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
Assembly Unit: Primary Assembly (GCF_943734724.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome XOX030905.1=NC_071325.1285
Chromosome 2OX030903.1=NC_071326.10
Chromosome 3OX030904.1=NC_071327.10

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule225,712,104288225,707,10484,416,232160
Chromosome XAllAssembled moleculeUnlocalized scaffolds48,950,81719,747,13929,203,678286128548,947,61719,746,93929,200,6781,146,93019,747,139274,936716000
Chromosome 2Assembled molecule92,345,055192,343,85592,345,05560
Chromosome 3Assembled molecule84,416,232184,415,63284,416,23230
MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
Mitochondrion MT15,361115,36115,36100