Agriopis marginaria
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Info
| NCBI taxon id: | 190331 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Geometridae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Geometroidea;Geometridae;Ennominae;Agriopis; |
| GoaT genome size (M): | 831 (ancestor) |
| GoaT asm span (M): | 500 (direct) |
| GoaT chr no.: | 62 (ancestor) |
| GoaT haploid no.: | 29 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilAgrMarg |
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 |
|---|---|---|---|---|---|---|
| ilAgrMarg1 | NHMUK014043062 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | ABDOMEN | SAMEA9359552 | SAMEA9359455 |
| ilAgrMarg1 | NHMUK014043062 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | THORAX | SAMEA9359551 | SAMEA9359455 |
| ilAgrMarg1 | NHMUK014043062 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | HEAD | SAMEA9359551 | SAMEA9359455 |
| ilAgrMarg2 | Ox001086 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA10200646 | SAMEA10107009 |
| ilAgrMarg2 | Ox001086 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA10200648 | SAMEA10107009 |
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 | ilAgrMarg1 | 31 | 17.14 | 492,432,860 | 28.42 | 1.58 | 98.74 | 0.16 |   histogram.txt |
| hic-arima2 | ilAgrMarg1 | 31 | 70.79 | 540,325,452 | 46.65 | 3.34 | 97.36 | 0.84 |   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 | ilAgrMarg1 | 2022-01-08 | 89257 | m64222e_220108_175153 | C01 | 1009 | 17,831,319,846 | 9,431 | SAMEA9359552 | ERR8575367 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| Hi-C - Arima v2 | ilAgrMarg1 | 2021-09-09 | 40634_4#1 | 820,616,738 | 123,913,127,438 | SAMEA9359551 | ERR8571649 | qc complete | Agriopis marginaria (1.00) |
| RNA PolyA | ilAgrMarg2 | 2022-08-23 | 45657_1#24 | 67,717,254 | 10,225,305,354 | SAMEA10200648 | ERR10123669 | qc complete | Agriopis marginaria (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 |
|---|---|
| 0.917245 | 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 |
|---|---|---|---|
| ilAgrMarg1 | atg000291l | 1119 |
|
| ilAgrMarg1 | ptg000001l | 1899 |
|
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 |
|---|---|
| ilAgrMarg1 |    |
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
ilAgrMarg1.hifiasm.20220205
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| ilAgrMarg1 | hifiasm.purging | 2022-02-05 | 18,344,939 | 50 | 517,104,520 | C:98.7%[S:96.2%,D:2.5%],F:0.4%,M:0.9%,n:1367 | Q64.5-C99.4(HiFi) | ||
| ilAgrMarg1 | hifiasm | 2022-02-05 | 18,344,939 | 74 | 528,073,500 | C:98.6%[S:93.3%,D:5.3%],F:0.4%,M:1.0%,n:1367 | Q64.4-C99.5(HiFi) | ||
| ilAgrMarg1 | hifiasm.scaffolding.salsa | 2022-02-05 | 16,019,797 | 61 | 19,680,586 | 47 | 517,111,520 | C:98.8%[S:96.5%,D:2.3%],F:0.4%,M:0.8%,n:1367 | Q64.5-C99.4(HiFi) |
| ilAgrMarg1 | hifiasm.scaffolding.yahs | 2022-02-05 | 15,329,000 | 68 | 19,376,663 | 45 | 517,109,120 | C:98.6%[S:96.6%,D:2.0%],F:0.4%,M:1.0%,n:1367 | Q64.5-C99.4(HiFi) |
| ilAgrMarg1 | hicanu | 2022-02-05 | 3,154,868 | 974 | 1,011,540,397 | C:98.9%[S:2.0%,D:96.9%],F:0.5%,M:0.6%,n:1367 | Q69.0-C99.5(HiFi) | ||
| ilAgrMarg1 | hicanu.purging | 2022-02-05 | 5,616,840 | 212 | 504,731,986 | C:98.6%[S:97.4%,D:1.2%],F:0.6%,M:0.8%,n:1367 | Q69.7-C99.5(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| ilAgrMarg1 | mitohifi.hifiasm | mito | 2022-02-05 | 16,942 | 36 | None | OK509075.1; 15,309 bp; 37 genes | |
| ilAgrMarg1 | mitohifi.hicanu | mito | 2022-02-05 | 16,941 | 36 | None | OK509075.1; 15,309 bp; 37 genes | |
| ilAgrMarg1 | mitohifi.reads | mito | 2022-02-05 | 31,974 | 57 | None | OK509075.1; 15,309 bp; 37 genes |
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