Thyatira batis
Peach blossom
Info
| NCBI taxon id: | 721163 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Drepanidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Drepanoidea;Drepanidae;Thyatirinae;Thyatira; |
| GoaT genome size (M): | 317 (ancestor) |
| GoaT asm span (M): | 314 (direct) |
| GoaT chr no.: | 62 (direct) |
| GoaT haploid no.: | 31 (direct) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilThyBati |
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 |
|---|---|---|---|---|---|---|
| ilThyBati1 | Ox000061 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7519961 | SAMEA7519923 |
| ilThyBati1 | Ox000061 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7519961 | SAMEA7519923 |
| ilThyBati1 | Ox000061 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7519961 | SAMEA7519923 |
| ilThyBati1 | Ox000061 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7519961 | SAMEA7519923 |
| ilThyBati1 | Ox000061 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7519961 | SAMEA7519923 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| pacbio | ilThyBati1 | 31 | 14.63 | 308,594,970 | 27.34 | 1.78 | 97.10 | 0.21 |   histogram.txt |
| 10x | ilThyBati1 | 31 | 53.8 | 337,371,976 | 35.37 | 2.15 | 97.14 | 0.50 |   histogram.txt |
| htag-sanger | ilThyBati1 | 31 | 10.14 | 320,517,422 | 27.70 | 2.04 | 99.41 | 0.30 |   histogram.txt |
| htag-marek | ilThyBati1 | 31 | 18.06 | 313,357,082 | 26.86 | 1.97 | 99.17 | 0.30 |   histogram.txt |
| hic-arima | ilThyBati1 | 31 | 63.94 | 595,925,911 | 0.00 | 50.11 | 1.29 | 0.25 |   histogram.txt |
| - | - | - | 0 | 0.00 | NaN | NaN | NaN |
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 | ilThyBati1 | 2019-10-16 | 72309 | m64016_191016_110433 | A01 | 1003 | 9,655,227,346 | 12,978 | SAMEA7519960 | ||
| PacBio - IsoSeq | ilThyBati2 | 2021-09-04 | TRACTION-RUN-63 | m64222e_210904_144241 | B01 | 1004 | 1,316,170,642 | 3,437 | SAMEA7701595 |
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 | ilThyBati1 | 2019-11-18 | 31782_7#2 | 80,962,890 | 12,225,396,390 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Chromium genome | ilThyBati1 | 2019-11-18 | 31782_7#3 | 96,514,188 | 14,573,642,388 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Chromium genome | ilThyBati1 | 2019-11-18 | 31782_7#4 | 99,851,174 | 15,077,527,274 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Chromium genome | ilThyBati1 | 2019-11-18 | 31782_7#1 | 109,611,974 | 16,551,408,074 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#73 | 5,613,888 | 833,662,368 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#81 | 4,361,506 | 647,683,641 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#78 | 4,919,680 | 730,572,480 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#76 | 6,034,354 | 896,101,569 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#77 | 5,548,680 | 823,978,980 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#83 | 4,687,742 | 696,129,687 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#74 | 5,854,460 | 869,387,310 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#82 | 4,954,232 | 735,703,452 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#75 | 4,159,870 | 617,740,695 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#84 | 4,280,930 | 635,718,105 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#80 | 4,575,106 | 679,403,241 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_1#79 | 4,995,956 | 741,899,466 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_2#43 | 9,476,482 | 1,407,257,577 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_2#39 | 8,873,850 | 1,317,766,725 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_2#38 | 9,120,110 | 1,354,336,335 | SAMEA7519960 | qc complete | Thyatira batis (1.00) | |
| Pre-quality controlled | ilThyBati1 | 2020-08-07 | 34781_2#44 | 8,667,170 | 1,287,074,745 | SAMEA7519960 | qc complete | Thyatira batis (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 |
|---|---|
| 0.910625 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, 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 |
|---|---|
| ilThyBati1 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| canu | ccs.purge | 2020-01-15 | 3,107,209 | 228 | 3,308,397 | 214 | 318,692,723 | C:97.6%[S:96.0%,D:1.6%],F:0.8%,M:1.6%,n:1658 | - |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
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