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Source database (GenBank or RefSeq) File type

ilCydAmpl1.1

Organism name:

Cydia amplana (moths)

BioSample:

SAMEA111458729

BioProject:

PRJEB59260

Submitter:

WELLCOME SANGER INSTITUTE

Date:

2023/02/03

Assembly type:

haploid (principal pseudohaplotype of diploid)

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_948474715.1 (latest)

RefSeq assembly accession:

GCF_948474715.1 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in GenBank: chromosome MT

Data displayed for RefSeq version

WGS Project:

CAOLDY01

Assembly method:

various

Genome coverage:

62x

Sequencing technology:

PacBio,Arima2

Linked assembly:

GCA_948473095.1 (alternate pseudohaplotype of diploid)

IDs: 15805161 [UID] 40580858 [GenBank] 53564378 [RefSeq]

See Genome Information for Cydia amplana

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_948474715.1	≠	GCF_948474715.1	ilCydAmpl1.1	Chromosome	Latest GenBank, Latest RefSeq

Comment

The assembly ilCydAmpl1.1 is based on 62x 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. Finally, the primary assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size.  more

Global statistics

Total sequence length	504,318,984
Total ungapped length	504,304,984
Gaps between scaffolds	0
Number of scaffolds	39
Scaffold N50	18,973,136
Scaffold L50	11
Number of contigs	109
Contig N50	8,695,702
Contig L50	20
Total number of chromosomes and plasmids	28
Number of component sequences (WGS or clone)	39

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	OX419655.1	=	NC_086069.1	0
Chromosome 2	OX419656.1	=	NC_086070.1	0
Chromosome 3	OX419657.1	=	NC_086071.1	0
Chromosome 4	OX419658.1	=	NC_086072.1	0
Chromosome 5	OX419659.1	=	NC_086073.1	0
Chromosome 6	OX419660.1	=	NC_086074.1	0
Chromosome 7	OX419661.1	=	NC_086075.1	0
Chromosome 8	OX419662.1	=	NC_086076.1	0
Chromosome 9	OX419663.1	=	NC_086077.1	0
Chromosome 10	OX419664.1	=	NC_086078.1	0
Chromosome 11	OX419665.1	=	NC_086079.1	0
Chromosome 12	OX419666.1	=	NC_086080.1	0
Chromosome 13	OX419667.1	=	NC_086081.1	0
Chromosome 14	OX419668.1	=	NC_086082.1	0
Chromosome 15	OX419669.1	=	NC_086083.1	0
Chromosome 16	OX419670.1	=	NC_086084.1	0
Chromosome 17	OX419671.1	=	NC_086085.1	0
Chromosome 18	OX419672.1	=	NC_086086.1	0
Chromosome 19	OX419673.1	=	NC_086087.1	0
Chromosome 20	OX419674.1	=	NC_086088.1	0
Chromosome 21	OX419675.1	=	NC_086089.1	0
Chromosome 22	OX419676.1	=	NC_086090.1	0
Chromosome 23	OX419677.1	=	NC_086091.1	0
Chromosome 24	OX419678.1	=	NC_086092.1	0
Chromosome 25	OX419679.1	=	NC_086093.1	0
Chromosome 26	OX419680.1	=	NC_086094.1	0
Chromosome 27	OX419681.1	=	NC_086095.1	0
Chromosome Z	OX419654.1	=	NC_086096.1	0
unplaced	n/a	n/a	n/a	11

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	504,318,984	39	504,304,984	18,973,136	70
Chromosome 1	30,377,450	1	30,376,450	30,377,450	5
Chromosome 2	26,834,566	1	26,833,966	26,834,566	3
Chromosome 3	23,130,647	1	23,129,447	23,130,647	6
Chromosome 4	22,371,603	1	22,370,803	22,371,603	4
Chromosome 5	21,296,765	1	21,295,965	21,296,765	4
Chromosome 6	20,638,857	1	20,638,057	20,638,857	4
Chromosome 7	20,552,724	1	20,552,524	20,552,724	1
Chromosome 8	19,926,398	1	19,926,198	19,926,398	1
Chromosome 9	18,979,233	1	18,979,233	18,979,233	0
Chromosome 10	18,973,136	1	18,972,536	18,973,136	3
Chromosome 11	18,605,246	1	18,604,846	18,605,246	2
Chromosome 12	18,215,254	1	18,214,654	18,215,254	3
Chromosome 13	17,664,527	1	17,663,527	17,664,527	5
Chromosome 14	17,615,700	1	17,615,300	17,615,700	2
Chromosome 15	17,380,361	1	17,379,161	17,380,361	6
Chromosome 16	16,776,504	1	16,775,904	16,776,504	3
Chromosome 17	16,731,639	1	16,731,439	16,731,639	1
Chromosome 18	16,699,241	1	16,699,041	16,699,241	1
Chromosome 19	15,469,522	1	15,469,522	15,469,522	0
Chromosome 20	13,098,915	1	13,098,515	13,098,915	2
Chromosome 21	12,945,012	1	12,944,812	12,945,012	1
Chromosome 22	12,268,687	1	12,268,487	12,268,687	1
Chromosome 23	11,592,465	1	11,592,265	11,592,465	1
Chromosome 24	9,588,978	1	9,588,378	9,588,978	3
Chromosome 25	9,531,776	1	9,531,176	9,531,776	3
Chromosome 26	8,965,926	1	8,965,726	8,965,926	1
Chromosome 27	7,942,088	1	7,942,088	7,942,088	0
Chromosome Z	39,759,656	1	39,758,856	39,759,656	4
unplaced	386,108	11	386,108	39,913	0

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ilCydAmpl1.1

See Genome Information for Cydia amplana

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

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