Eristalinus sepulchralis
Small Spotty-eyed Dronefly
Info
| NCBI taxon id: | 2725509 NCBI; ENA; GoaT |
|---|---|
| Order: | Diptera |
| Family: | Syrphidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Syrphoidea;Syrphidae;Eristalinae;Eristalini;Eristalinus; |
| GoaT genome size (M): | 528 (ancestor) |
| GoaT asm span (M): | 376 (direct) |
| GoaT chr no.: | 12 (direct) |
| GoaT haploid no.: | 6 (direct) |
| GoaT ploidy: | 3 (ancestor) |
| ToLID prefix: | idEriSepu |
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 |
|---|---|---|---|---|---|---|
| idEriSepu1 | Ox000764 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7746571 | SAMEA7746477 |
| idEriSepu1 | Ox000764 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7746572 | SAMEA7746477 |
| idEriSepu1 | Ox000764 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7746573 | SAMEA7746477 |
| idEriSepu2 | NHMUK014036950 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | ABDOMEN | SAMEA14448854 | SAMEA110029158 |
| idEriSepu2 | NHMUK014036950 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | THORAX | SAMEA14448853 | SAMEA110029158 |
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 | idEriSepu1 | 31 | 22.2 | 293,005,658 | 15.26 | 2.59 | 97.03 | 0.48 |   histogram.txt |
| hic-arima2 | idEriSepu1 | 31 | 161 | 437,730,556 | 127.94 | 43.55 | 96.89 | 0.49 |   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 | idEriSepu1 | 2021-08-12 | 85513 | m64222e_210812_111413 | A01 | 1015 | 15,131,340,430 | 11,400 | SAMEA7746573 | ERR9863244 |
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 | idEriSepu1 | 2021-03-26 | 36940_4#3 | 1,355,438,540 | 204,671,219,540 | SAMEA7746571 | ERR9866432 | qc complete | Eristalinus sepulchralis (1.00) |
| RNA PolyA | idEriSepu2 | 2022-09-29 | 45898_4#5 | 104,903,654 | 15,840,451,754 | SAMEA14448853 | ERR10378014 | qc complete | Eristalinus sepulchralis (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 |
|---|---|
| 0.91333 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.907417 | [149 seqs] NZ_LKLU01000066.1 Lactococcus lactis subsp. lactis strain M20 contig_0, whole genome shotgun sequence [...] |
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 |
|---|---|
| idEriSepu1 |    |
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
idEriSepu1.hifiasm.20220207
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| idEriSepu1 | hifiasm.purging | 2022-02-07 | 5,609,999 | 384 | 376,917,788 | C:99.3%[S:98.9%,D:0.4%],F:0.1%,M:0.6%,n:1367 | Q60.8-C98.6(HiFi) | ||
| idEriSepu1 | hifiasm | 2022-02-07 | 4,975,978 | 848 | 410,411,829 | C:99.3%[S:98.8%,D:0.5%],F:0.1%,M:0.6%,n:1367 | Q59.4-C99.1(HiFi) | ||
| idEriSepu1 | hifiasm.scaffolding.salsa | 2022-02-07 | 5,534,442 | 387 | 38,579,861 | 282 | 376,970,288 | C:99.3%[S:98.9%,D:0.4%],F:0.1%,M:0.6%,n:1367 | Q60.8-C98.6(HiFi) |
| idEriSepu1 | hifiasm.scaffolding.yahs | 2022-02-07 | 5,609,999 | 390 | 123,948,156 | 277 | 376,940,388 | C:99.3%[S:98.9%,D:0.4%],F:0.1%,M:0.6%,n:1367 | Q60.8-C98.6(HiFi) |
| idEriSepu1 | hicanu.purging | 2022-02-07 | 3,464,918 | 742 | 381,633,508 | C:99.4%[S:99.0%,D:0.4%],F:0.1%,M:0.5%,n:1367 | Q67.7-C98.8(HiFi) | ||
| idEriSepu1 | hicanu | 2022-02-07 | 2,853,196 | 2,249 | 781,849,184 | C:99.6%[S:2.2%,D:97.4%],F:0.0%,M:0.4%,n:1367 | Q67.8-C99.2(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| idEriSepu1 | mitohifi.hifiasm | mito | 2022-02-07 | 15,960 | 37 | None | MT942687.1; 15,883 bp; 37 genes | |
| idEriSepu1 | mitohifi.hicanu | mito | 2022-02-07 | 15,962 | 37 | None | MT942687.1; 15,883 bp; 37 genes | |
| idEriSepu1 | mitohifi.reads | mito | 2022-02-07 | 15,976 | 36 | COX2 | MT942687.1; 15,883 bp; 37 genes |
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