Helophilus pendulus
Tiger hoverfly
Info
| NCBI taxon id: | 226174 |
|---|---|
| Order: | Diptera |
| Family: | Syrphidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Syrphoidea;Syrphidae;Eristalinae;Eristalini;Helophilus; |
| GoaT genome size (M): | 528 (ancestor) |
| GoaT asm span (M): | 466 (ancestor) |
| GoaT chr no.: | 12 (direct) |
| GoaT ploidy: | 3 (ancestor) |
| ToLID prefix: | idHelPend |
Specimens
Below is information about specimens collected for this species retrieved from the Golden Record manifest.
public_name | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| idHelPend1 | Ox000157 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7520143 | SAMEA7520048 |
| idHelPend1 | Ox000157 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7520143 | SAMEA7520048 |
| idHelPend1 | Ox000157 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7520144 | SAMEA7520048 |
| idHelPend2 | Ox000169 | UNIVERSITY OF OXFORD | MALE | ABDOMEN | SAMEA7520146 | SAMEA7520049 |
| idHelPend2 | Ox000169 | UNIVERSITY OF OXFORD | MALE | THORAX | SAMEA7520145 | SAMEA7520049 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope.
source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| 10x | idHelPend2 | 31 | 36.1 | 521,548,647 | 41.92 | 2.28 | 95.99 | 0.46 |   |
| pacbio | idHelPend2 | 31 | 6.995 | 430,807,897 | 27.31 | 2.29 | 99.20 | 0.21 |   |
| hic-arima2 | idHelPend4 | 31 | 76.11 | 547,883,598 | 0.00 | 100.00 | 1.72 | 0.24 |   |
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 | idHelPend2 | 2020-01-13 | TRACTION-RUN-6 | m64097_200113_175438 | D01 | 1022 | 6,437,159,164 | 15,831 | SAMEA7520145 |
Illumina run data
Illumina run stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | idHelPend2 | 2020-02-10 | 32979_5#6 | 88,460,456 | 13,357,528,856 | SAMEA7520145 | qc complete | Helophilus pendulus (1.00) | |
| Chromium genome | idHelPend2 | 2020-02-10 | 32979_5#7 | 90,411,456 | 13,652,129,856 | SAMEA7520145 | qc complete | Helophilus pendulus (1.00) | |
| Chromium genome | idHelPend2 | 2020-02-10 | 32979_5#8 | 106,202,570 | 16,036,588,070 | SAMEA7520145 | qc complete | Helophilus pendulus (1.00) | |
| Chromium genome | idHelPend2 | 2020-02-10 | 32979_5#5 | 112,184,136 | 16,939,804,536 | SAMEA7520145 | qc complete | Helophilus pendulus (1.00) | |
| Hi-C - Arima v2 | idHelPend4 | 2023-07-14 | 47478_1#7 | 741,822,572 | 112,015,208,372 | SAMEA8534327 | qc complete | Helophilus pendulus (1.00) | |
| RNA PolyA | idHelPend1 | 2023-08-07 | 47706_1#35 | 57,782,496 | 8,725,156,896 | SAMEA7520144 | qc complete | Helophilus pendulus (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 |
|---|---|
| 0.925107 | [36 seqs] NZ_AYYQ01000001.1 Lactobacillus ozensis DSM 23829 = JCM 17196 strain DSM 23829 NODE_1, whole genome shotgun sequence [...] |
| 0.901759 | 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 |
|---|---|
| idHelPend2 |    |
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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