Stenocranus minutus
Info
| NCBI taxon id: | 2794002 |
|---|---|
| Order: | Hemiptera |
| Family: | Delphacidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Auchenorrhyncha;Fulgoroidea;Delphacidae;Stenocraninae;Stenocranus; |
| GoaT genome size (M): | 601 (ancestor) |
| GoaT asm span (M): | 668 (ancestor) |
| GoaT chr no.: | 36 (ancestor) |
| ToLID prefix: | ihSteMinu |
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 |
|---|---|---|---|---|---|---|
| ihSteMinu1 | NHMUK014446340 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7849498 | SAMEA7849414 |
| ihSteMinu2 | NHMUK014446341 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7849499 | SAMEA7849415 |
| ihSteMinu3 | NHMUK014446339 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7849497 | SAMEA7849413 |
| ihSteMinu4 | NHMUK014444837 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | MID_BODY | SAMEA8534374 | SAMEA8534342 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| hic-arima2 | ihSteMinu2 | 31 | 20.69 | 2,608,012,077 | 70.93 | 0.89 | 98.50 | 0.20 |   |
| pacbio | ihSteMinu1 | 31 | 35.34 | 12,639,077 | 86.98 | 3.50 | 86.62 | 3.61 |   |
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 | ihSteMinu1 | 2021-04-09 | 81227 | m64228e_210409_131148 | A01 | 1003 | 2,796,304,279 | 14,121 | SAMEA7849498 |
Illumina run data
Illumina run stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Hi-C - Arima v2 | ihSteMinu2 | 2021-03-30 | 37019_3#3 | 946,723,328 | 142,955,222,528 | SAMEA7849499 | qc complete | Stenocranus minutus (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 |
|---|---|
| 0.973506 | [20 seqs] NZ_JRLH01000001.1 Arsenophonus endosymbiont str. Hangzhou of Nilaparvata lugens strain Hangzhou contig1, whole genome shotgun sequence [...] |
| 0.917777 | NC_011551.1 Bacteriophage APSE-2, complete genome |
| 0.913621 | [94 seqs] NZ_LWMI01000001.1 Candidatus Arsenophonus triatominarum strain ATi contig000001, whole genome shotgun sequence [...] |
| 0.910001 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
Species composition by small subunit (SSU) presence in the assembly.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
Re-assembly of reads classified under each identified SSU Marker family.
specimen | family | classified reads | original assembly | re-assembly | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | reads | BUSCO | contigs | contig length | additional reads | circos | ||
| No matching records found | |||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| ihSteMinu1 |    |
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 MitoHiFi2.
specimen | asm | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|
| No matching records found | |||||||
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