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gfArmOsto1.1

Organism name:
Armillaria ostoyae (basidiomycete fungi)
BioSample:
SAMEA110449800
BioProject:
PRJEB75315
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2024/04/27
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_964034915.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CAXIUH01
Assembly method:
various
Genome coverage:
371x
Sequencing technology:
PacBio,Arima2
Linked assembly:
GCA_964034935.1 (alternate pseudohaplotype of diploid)

IDs: 22457941 [UID] 56963618 [GenBank]

See Genome Information for Armillaria ostoyae

There are 4 assemblies for this organism

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History (Show revision history)

Comment

The assembly gfArmOsto1.1 is based on 371x PacBio data and Arima2 Hi-C data generated by the Darwin Tree of Life Project
(https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation ... with purge_dups, and Hi-C based scaffolding with YaHS. The mitochondrial genome was assembled using MitoHiFi and OATK. Finally, the primary assembly was analysed and manually improved using TreeVal. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size.  more

Global statistics

Total sequence length66,261,395
Total ungapped length66,251,695
Gaps between scaffolds0
Number of scaffolds440
Scaffold N504,706,541
Scaffold L506
Number of contigs500
Contig N501,272,619
Contig L5016
Total number of chromosomes and plasmids12
Number of component sequences (WGS or clone)440

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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 (GCA_964034914.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OZ035941.1n/an/a0
Chromosome 2OZ035942.1n/an/a1
Chromosome 3OZ035943.1n/an/a0
Chromosome 4OZ035944.1n/an/a1
Chromosome 5OZ035945.1n/an/a1
Chromosome 6OZ035946.1n/an/a1
Chromosome 7OZ035947.1n/an/a0
Chromosome 8OZ035948.1n/an/a1
Chromosome 9OZ035949.1n/an/a1
Chromosome 10OZ035950.1n/an/a0
Chromosome 11OZ035951.1n/an/a1
unplacedn/an/an/a421

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule66,148,02643966,138,3264,706,541600
Chromosome 1Assembled molecule6,509,27716,507,5776,509,277100
Chromosome 2AllAssembled moleculeUnlocalized scaffolds6,218,4776,093,814124,6632116,217,7776,093,114124,6636,093,8146,093,814124,663440000
Chromosome 3Assembled molecule5,841,62515,840,5255,841,62560
Chromosome 4AllAssembled moleculeUnlocalized scaffolds5,508,2835,434,70273,5812115,507,7835,434,20273,5815,434,7025,434,70273,581330000
Chromosome 5AllAssembled moleculeUnlocalized scaffolds5,445,4475,374,64670,8012115,445,2475,374,44670,8015,374,6465,374,64670,801220000
Chromosome 6AllAssembled moleculeUnlocalized scaffolds4,715,9114,286,477429,4342114,714,3114,284,977429,3344,286,4774,286,477429,43412111000
Chromosome 7Assembled molecule4,706,54114,706,1414,706,54120
Chromosome 8AllAssembled moleculeUnlocalized scaffolds4,513,0584,356,368156,6902114,512,4584,355,768156,6904,356,3684,356,368156,690440000
Chromosome 9AllAssembled moleculeUnlocalized scaffolds4,448,4054,438,31810,0872114,447,2054,437,11810,0874,438,3184,438,31810,087770000
Chromosome 10Assembled molecule3,963,34313,962,4433,963,34350
Chromosome 11AllAssembled moleculeUnlocalized scaffolds3,929,2343,744,856184,3782113,928,4343,744,056184,3783,744,8563,744,856184,378550000
unplacedAssembled molecule10,348,42542110,348,42523,99500
MoleculeTotal
Length
Mitochondrion MT113,369