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bCatUst1.pri

Organism name:
Catharus ustulatus (Swainson's thrush)
Isolate:
bCatUst1
Sex:
female
BioSample:
SAMN12618602
BioProject:
PRJNA561933
Submitter:
Vertebrate Genomes Project
Date:
2019/12/31
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_009819885.1 (replaced)
RefSeq assembly accession:
GCF_009819885.1 (suppressed) see latest RefSeq assembly for this species
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for GenBank version
WGS Project:
WNMQ01
Assembly method:
FALCON v. 2018.31.08-03.06; FALCON-Unzip v. 6.0.0.47841; purge_haplotigs v. v1.0.3+ 1.Nov.2018; scaff10x v. 2; Bionano Solve DLS v. 3.2.1; Salsa HiC v. 2.2; Arrow smrtanalysis Pacbio polishing & gap filling v. 6.0.0.47841; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; gEVAL manual curation v. 2019-09-24; VGP assembly pipeline individual v. 1.5
Expected final version:
no
Genome coverage:
60.58x
Sequencing technology:
PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS
Linked assembly:
GCA_009819505.1 (alternate pseudohaplotype of diploid)

IDs: 5428251 [UID] 15715208 [GenBank] 17765058 [RefSeq]

See Genome Information for Catharus ustulatus

Pathogen Detection Resources

There are 2 assemblies for this organism

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History (Show revision history)

Comment

This assembly represents the principal haplotype of the diploid genome Catharus ustulatus and includes the chromosomes. The alternate haplotype sequences are in WGS project WNMR00000000

Global statistics

Total sequence length1,131,635,156
Total ungapped length1,118,731,561
Gaps between scaffolds0
Number of scaffolds162
Scaffold N5063,528,738
Scaffold L506
Number of contigs590
Contig N504,908,935
Contig L5070
Total number of chromosomes and plasmids43
Number of component sequences (WGS or clone)162

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Assembly Information

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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_009819895.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM020336.1=NC_046221.10
Chromosome 2CM020337.1=NC_046222.10
Chromosome 3CM020338.1=NC_046223.10
Chromosome 4CM020339.1=NC_046224.10
Chromosome 5CM020340.1=NC_046225.10
Chromosome 6CM020341.1=NC_046226.10
Chromosome 7CM020342.1=NC_046227.10
Chromosome 8CM020343.1=NC_046228.10
Chromosome 9CM020344.1=NC_046229.10
Chromosome 10CM020345.1=NC_046230.10
Chromosome 11CM020346.1=NC_046231.10
Chromosome 12CM020347.1=NC_046232.10
Chromosome 13CM020348.1=NC_046233.10
Chromosome 14CM020349.1=NC_046234.10
Chromosome 15CM020350.1=NC_046235.10
Chromosome 16CM020351.1=NC_046236.10
Chromosome 17CM020352.1=NC_046237.10
Chromosome 18CM020353.1=NC_046238.10
Chromosome 19CM020354.1=NC_046239.10
Chromosome 20CM020355.1=NC_046240.10
Chromosome 21CM020356.1=NC_046241.10
Chromosome 22CM020357.1=NC_046242.10
Chromosome 23CM020358.1=NC_046243.10
Chromosome 24CM020359.1=NC_046244.10
Chromosome 25CM020360.1=NC_046245.10
Chromosome 26CM020361.1=NC_046246.10
Chromosome 27CM020362.1=NC_046247.10
Chromosome 28CM020363.1=NC_046248.10
Chromosome 29CM020364.1=NC_046249.10
Chromosome 30CM020365.1=NC_046250.10
Chromosome 31CM020366.1=NC_046251.10
Chromosome 32CM020367.1=NC_046252.10
Chromosome 33CM020368.1=NC_046253.10
Chromosome 34CM020369.1=NC_046254.10
Chromosome 35CM020370.1=NC_046255.10
Chromosome 36CM020371.1=NC_046256.10
Chromosome 37CM020372.1=NC_046257.10
Chromosome 38CM020373.1=NC_046258.10
Chromosome 39CM020374.1=NC_046259.10
Chromosome 40CM020375.1=NC_046260.10
Chromosome WCM020377.1=NC_046261.12
Chromosome ZCM020376.1=NC_046262.10
unplacedn/an/an/a117

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule1,131,616,4301611,118,712,83563,528,7384280
Chromosome 1Assembled molecule165,774,2571165,167,040165,774,257500
Chromosome 2Assembled molecule124,776,7411123,659,124124,776,741440
Chromosome 3Assembled molecule120,187,5231119,345,590120,187,523310
Chromosome 4Assembled molecule77,026,709176,887,75877,026,709240
Chromosome 5Assembled molecule76,913,702176,911,59876,913,702240
Chromosome 6Assembled molecule63,528,738163,527,76063,528,738150
Chromosome 7Assembled molecule40,436,149140,382,83940,436,14990
Chromosome 8Assembled molecule36,548,054136,547,52836,548,05470
Chromosome 9Assembled molecule33,537,716133,537,15133,537,716100
Chromosome 10Assembled molecule26,454,946126,454,40726,454,94680
Chromosome 11Assembled molecule22,310,542122,165,88622,310,54280
Chromosome 12Assembled molecule21,745,260121,745,12121,745,26040
Chromosome 13Assembled molecule21,568,194121,568,05521,568,19440
Chromosome 14Assembled molecule20,997,689120,997,35020,997,68960
Chromosome 15Assembled molecule19,392,598119,392,25919,392,59860
Chromosome 16Assembled molecule16,676,293116,675,89316,676,29340
Chromosome 17Assembled molecule15,618,554115,618,22815,618,55450
Chromosome 18Assembled molecule14,366,659114,366,23314,366,65960
Chromosome 19Assembled molecule12,285,394112,284,99412,285,39440
Chromosome 20Assembled molecule12,176,784112,176,57112,176,78430
Chromosome 21Assembled molecule11,336,639111,336,42611,336,63930
Chromosome 22Assembled molecule11,098,648111,098,54811,098,64810
Chromosome 23Assembled molecule8,847,85017,034,6908,847,85090
Chromosome 24Assembled molecule8,463,71618,463,6038,463,71620
Chromosome 25Assembled molecule8,277,58717,279,8998,277,58730
Chromosome 26Assembled molecule7,731,92617,731,7137,731,92630
Chromosome 27Assembled molecule7,348,43715,584,0027,348,43750
Chromosome 28Assembled molecule6,915,65816,915,4586,915,65820
Chromosome 29Assembled molecule6,627,22616,626,5266,627,22630
Chromosome 30Assembled molecule4,023,37913,846,2144,023,37940
Chromosome 31Assembled molecule3,655,33813,654,1383,655,33840
Chromosome 32Assembled molecule2,810,27912,807,8792,810,27980
Chromosome 33Assembled molecule2,284,36212,283,9622,284,36240
Chromosome 34Assembled molecule1,869,54611,868,6461,869,54650
Chromosome 35Assembled molecule1,647,61411,646,8141,647,61440
Chromosome 36Assembled molecule1,644,51411,643,6141,644,51450
Chromosome 37Assembled molecule1,317,71111,316,7111,317,71160
Chromosome 38Assembled molecule955,8461955,346955,84610
Chromosome 39Assembled molecule928,4671927,667928,46740
Chromosome 40Assembled molecule904,8021904,002904,80240
Chromosome WAllAssembled moleculeUnlocalized scaffolds34,358,57522,446,48511,912,09031229,443,39519,325,78610,117,60922,446,48522,446,4858,213,30718108000
Chromosome ZAssembled molecule46,015,489145,780,83046,015,48980
unplacedAssembled molecule10,230,31911710,151,367166,000500
MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
Mitochondrion MT18,726118,72618,72600