Apatura iris
Purple emperor
Info
| NCBI taxon id: | 191396 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Nymphalidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Papilionoidea;Nymphalidae;Apaturinae;Apatura; |
| GoaT genome size (M): | 381 (ancestor) |
| GoaT asm span (M): | 424 (ancestor) |
| GoaT chr no.: | 62 (ancestor) |
| GoaT haploid no.: | 31 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilApaIris |
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 |
|---|---|---|---|---|---|---|
| ilApaIris1 | SAN0000763 | SANGER INSTITUTE | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7523211 | SAMEA7523112 |
| ilApaIris2 | SAN0000764 | SANGER INSTITUTE | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7523212 | SAMEA7523113 |
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 | ilApaIris1 | 31 | 45.24 | 465,881,520 | 30.09 | 0.47 | 95.62 | 0.44 |   histogram.txt |
| pacbio | ilApaIris1 | 31 | 21.85 | 410,259,693 | 20.34 | 0.44 | 99.20 | 0.19 |   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 | ilApaIris1 | 2019-12-07 | 73527 | m64016_191207_184901 | B01 | 1009 | 19,079,506,755 | 13,962 | SAMEA7523211 | ERR12512753 |
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 | ilApaIris1 | 2020-02-05 | 33032_8#5 | 105,147,416 | 15,877,259,816 | SAMEA7523211 | ERR12374315 | qc complete | Apatura iris (1.00) |
| Chromium genome | ilApaIris1 | 2020-02-05 | 33032_8#6 | 106,863,232 | 16,136,348,032 | SAMEA7523211 | ERR12374316 | qc complete | Apatura iris (1.00) |
| Chromium genome | ilApaIris1 | 2020-02-05 | 33032_8#7 | 115,769,880 | 17,481,251,880 | SAMEA7523211 | ERR12374317 | qc complete | Apatura iris (1.00) |
| Chromium genome | ilApaIris1 | 2020-02-05 | 33032_8#8 | 113,701,492 | 17,168,925,292 | SAMEA7523211 | ERR12374318 | qc complete | Apatura iris (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 |
|---|---|
| 0.942602 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.91391 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.911545 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
| 0.910933 | NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome |
| 0.910001 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.909369 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.905724 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.903242 | [777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...] |
| 0.903242 | NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome |
| 0.901759 | [2 seqs] NC_004344.2 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis DNA, 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 |
|---|---|
| ilApaIris1 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| ilApaIris1 | hicanu | 2020-10-18 | 424,091 | 6,085 | 868,280,702 | C:98.0%[S:11.7%,D:86.3%],F:0.4%,M:1.6%,n:1658 | - | ||
| ilApaIris1 | hicanu.purging | 2020-10-18 | 11,866,186 | 152 | 407,294,778 | C:98.4%[S:98.1%,D:0.3%],F:0.5%,M:1.1%,n:1658 | - | ||
| ilApaIris1 | hifiasm.purging | 2020-10-18 | 14,581,730 | 43 | 406,734,682 | C:98.5%[S:98.1%,D:0.4%],F:0.4%,M:1.1%,n:1658 | - | ||
| ilApaIris1 | hifiasm | 2020-10-18 | 14,581,730 | 215 | 412,333,682 | C:98.7%[S:98.3%,D:0.4%],F:0.4%,M:0.9%,n:1658 | - | ||
| falcon | ccs.2-asm-falcon | 2019-12-12 | 13,329,611 | 62 | 13,329,611 | 59 | 406,120,016 | C:98.4%[S:98.0%,D:0.4%],F:0.5%,M:1.1%,n:1658 | - |
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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