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bChiLan1.pri

Organism name:
Chiroxiphia lanceolata (lance-tailed manakin)
Isolate:
bChiLan1
Sex:
female
BioSample:
SAMN12620979
BioProject:
PRJNA561943
Submitter:
Vertebrate Genomes Project
Date:
2020/01/03
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_009829145.1 (latest)
RefSeq assembly accession:
GCF_009829145.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
WNMC01
Assembly method:
FALCON v. DNANexus 1.9.0; FALCON-Unzip v. DNANexus 1.0.6; purge_haplotigs v. v1.0.3+ 1.Nov.2018; scaff10x v. 4.1.0; 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. 2019-10-08; VGP assembly pipeline v. 1.5
Expected final version:
no
Genome coverage:
67.75x
Sequencing technology:
PacBio Sequel I CLR; llumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS
Linked assembly:
GCA_009829205.1 (alternate pseudohaplotype of diploid)

IDs: 5432791 [UID] 15730398 [GenBank] 16053978 [RefSeq]

See Genome Information for Chiroxiphia lanceolata

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 Chiroxiphia lanceolata and includes the chromosomes. The alternate haplotype sequences are in WGS project WNMD00000000

Global statistics

Total sequence length1,089,631,598
Total ungapped length1,086,328,087
Gaps between scaffolds0
Number of scaffolds93
Scaffold N5075,608,808
Scaffold L505
Number of contigs299
Contig N5018,496,167
Contig L5017
Total number of chromosomes and plasmids35
Number of component sequences (WGS or clone)93

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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
Assembly Unit: Primary Assembly (GCF_009829265.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM020533.1=NC_045637.10
Chromosome 2CM020534.1=NC_045638.10
Chromosome 3CM020535.1=NC_045639.10
Chromosome 4CM020536.1=NC_045640.10
Chromosome 5CM020537.1=NC_045641.10
Chromosome 6CM020538.1=NC_045642.10
Chromosome 7CM020539.1=NC_045643.10
Chromosome 8CM020540.1=NC_045644.10
Chromosome 9CM020541.1=NC_045645.10
Chromosome 10CM020542.1=NC_045646.10
Chromosome 11CM020543.1=NC_045647.10
Chromosome 12CM020544.1=NC_045648.10
Chromosome 13CM020545.1=NC_045649.10
Chromosome 14CM020546.1=NC_045650.10
Chromosome 15CM020547.1=NC_045651.10
Chromosome 16CM020548.1=NC_045652.10
Chromosome 17CM020549.1=NC_045653.10
Chromosome 18CM020550.1=NC_045654.10
Chromosome 19CM020551.1=NC_045655.10
Chromosome 20CM020552.1=NC_045656.10
Chromosome 21CM020553.1=NC_045657.10
Chromosome 22CM020554.1=NC_045658.10
Chromosome 23CM020555.1=NC_045659.10
Chromosome 24CM020556.1=NC_045660.10
Chromosome 25CM020557.1=NC_045661.10
Chromosome 26CM020558.1=NC_045662.10
Chromosome 27CM020559.1=NC_045663.10
Chromosome 28CM020560.1=NC_045664.10
Chromosome 29CM020561.1=NC_045665.10
Chromosome 30CM020562.1=NC_045666.10
Chromosome 31CM020563.1=NC_045667.10
Chromosome 32CM020564.1=NC_045668.10
Chromosome 33CM020565.1=NC_045669.10
Chromosome WCM020567.1=NC_045670.116
Chromosome ZCM020566.1=NC_045671.10
unplacedn/an/an/a42

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule1,089,631,598931,086,328,08775,608,8082060
Chromosome 1Assembled molecule156,344,5571156,279,532156,344,557200
Chromosome 2Assembled molecule120,403,8951120,224,350120,403,895150
Chromosome 3Assembled molecule117,283,9551117,280,542117,283,955190
Chromosome 4Assembled molecule75,848,047175,687,12075,848,047220
Chromosome 5Assembled molecule75,608,808175,443,32075,608,80880
Chromosome 6Assembled molecule65,727,516165,726,21665,727,51690
Chromosome 7Assembled molecule39,976,536139,976,23639,976,53630
Chromosome 8Assembled molecule37,671,732137,671,23237,671,73210
Chromosome 9Assembled molecule31,492,288131,492,08831,492,28810
Chromosome 10Assembled molecule26,476,675126,476,57526,476,67510
Chromosome 11Assembled molecule22,063,292122,063,29222,063,29200
Chromosome 12Assembled molecule21,528,746121,528,74621,528,74600
Chromosome 13Assembled molecule21,201,277121,201,27721,201,27700
Chromosome 14Assembled molecule20,729,622120,729,52220,729,62210
Chromosome 15Assembled molecule19,292,269119,292,16919,292,26910
Chromosome 16Assembled molecule16,875,743116,875,54316,875,74320
Chromosome 17Assembled molecule15,378,035115,378,03515,378,03500
Chromosome 18Assembled molecule15,077,643115,077,44315,077,64320
Chromosome 19Assembled molecule12,698,277112,697,97712,698,27730
Chromosome 20Assembled molecule11,790,217111,790,01711,790,21720
Chromosome 21Assembled molecule11,781,312111,781,31211,781,31200
Chromosome 22Assembled molecule8,077,24618,076,5468,077,24630
Chromosome 23Assembled molecule7,394,70517,394,6057,394,70510
Chromosome 24Assembled molecule7,312,99817,312,7987,312,99820
Chromosome 25Assembled molecule6,921,62816,921,5286,921,62810
Chromosome 26Assembled molecule6,726,37016,726,0576,726,37040
Chromosome 27Assembled molecule6,261,57716,260,6776,261,57750
Chromosome 28Assembled molecule5,392,57215,391,8725,392,57250
Chromosome 29Assembled molecule2,725,28912,723,5912,725,28950
Chromosome 30Assembled molecule2,418,19912,414,9992,418,199120
Chromosome 31Assembled molecule770,1561768,956770,15640
Chromosome 32Assembled molecule746,2051745,632746,20520
Chromosome 33Assembled molecule702,6281702,628702,62800
Chromosome WAllAssembled moleculeUnlocalized scaffolds20,308,85616,093,8164,215,0401711618,290,25414,077,5144,212,74016,093,81616,093,816587,67812111000
Chromosome ZAssembled molecule75,361,692174,671,72975,361,692220
unplacedAssembled molecule3,261,035423,253,671180,651180