Callophrys rubi
Green hairstreak
Info
| NCBI taxon id: | 242269 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Lycaenidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Papilionoidea;Lycaenidae;Theclinae;Callophrys; |
| GoaT genome size (M): | 224 (ancestor) |
| GoaT asm span (M): | 633 (ancestor) |
| GoaT chr no.: | 46 (direct) |
| GoaT haploid no.: | 23 (direct) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilCalRubi |
Specimens
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
tolid | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| ilCalRubi1 | SAN0000765 | SANGER INSTITUTE | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7523213 | SAMEA7523114 |
| ilCalRubi2 | SAN0000934 | SANGER INSTITUTE | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7523456 | SAMEA7523357 |
| ilCalRubi3 | SAN0000935 | SANGER INSTITUTE | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7523457 | SAMEA7523358 |
| ilCalRubi4 | SAN0001688 | SANGER INSTITUTE | FEMALE | WHOLE_ORGANISM | SAMEA9700888 | SAMEA9700883 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.
source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| 10x | ilCalRubi2 | 31 | 16.85 | 904,690,455 | 38.73 | 2.18 | 99.22 | 0.52 |   histogram.txt |
| pacbio | ilCalRubi2 | 31 | 7.542 | 857,050,540 | 33.98 | 2.07 | 98.70 | 0.19 |   histogram.txt |
| pacbio | ilCalRubi4 | 31 | 36.33 | 22,763,317 | 87.85 | 3.25 | 86.37 | 4.60 |   histogram.txt |
Sequence data
PacBio run data
Below are stats for each PacBio seqeuncing run collected for this species.
pipeline | specimen | date | run id | movie | well | tag | yield | N50 | sample accession | run accession | barcode |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PacBio - HiFi | ilCalRubi2 | 2020-05-26 | TRACTION-RUN-36 | m64125_200526_150526 | A01 | 1019 | 13,765,535,720 | 12,766 | SAMEA7523456 | ||
| PacBio - HiFi | ilCalRubi4 | 2023-08-09 | TRACTION-RUN-751 | m64228e_230809_143706 | A01 | 2088 | 7,140,684,556 | 13,782 | SAMEA9700888 |
ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
pipeline | specimen | date | run id | flowcell | type | yield | N50 | sample accession | report |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Illumina run data
Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | ilCalRubi2 | 2020-10-08 | 35147_3#1 | 80,587,652 | 12,168,735,452 | SAMEA7523456 | qc complete | Callophrys rubi (1.00) | |
| Chromium genome | ilCalRubi2 | 2020-10-08 | 35147_3#3 | 101,999,116 | 15,401,866,516 | SAMEA7523456 | qc complete | Callophrys rubi (1.00) | |
| Chromium genome | ilCalRubi2 | 2020-10-08 | 35147_3#4 | 72,842,918 | 10,999,280,618 | SAMEA7523456 | qc complete | Callophrys rubi (1.00) | |
| Chromium genome | ilCalRubi2 | 2020-10-08 | 35147_3#2 | 71,930,890 | 10,861,564,390 | SAMEA7523456 | qc complete | Callophrys rubi (1.00) | |
| RNA PolyA | ilCalRubi3 | 2021-03-19 | 36703_8#9 | 42,799,392 | 6,462,708,192 | SAMEA7523457 | qc complete | Callophrys rubi (1.00) |
Cobionts
Below are results from a screen of the PacBio data using Mash screen against RefSeq assemblies. Only results with identity over 90% are displayed.
identity | info |
|---|---|
| 0.926662 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.910625 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.909686 | [833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, whole genome shotgun sequence [...] |
| 0.907417 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.906747 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
| 0.903242 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.902507 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.901 | NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
MarkerScan cobiont assembly by read separation based on observed families (see above). These reads are both aligned to the assembly and independently re-assembled. The quality of these assemblies is assessed by their completeness according to BUSCO, their span and the number of reads they encompass. For more information here.
specimen | family | classified reads | original assembly | re-assembly | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | number of reads | BUSCO | contigs | contig length | number of reads | ||
| No matching records found | ||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| ilCalRubi2 |    |
Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.
Features (colours represent quantile bins):
- Hexamer: Estimated coding density (expected to be higher in microbes than in animals).
- FastK: The median number of times each 60-mer in the sequence occures across the whole assembly (illustrates repetitiveness)
- Unique_15mers: Number of unique 15-mers per base pair (illustrates sequence diversity)
- Is_Connected: Presence of at least one Hi-C connection to another scaffold (absence of connections can indicate contamination)
- Connections_Base: Number of Hi-C connections per base pair
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| No matching records found | ||||||||
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