NCBI taxon id: | 1223885 |
---|---|
Order: | Hemiptera |
Family: | Cicadellidae |
NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Auchenorrhyncha;Membracoidea;Cicadellidae;Deltocephalinae;Opsius; |
GoaT genome size (M): | 4,658 (ancestor) |
GoaT asm span (M): | 745 (ancestor) |
GoaT chr no.: | 21 (ancestor) |
ToLID prefix: | ihOpsStac |
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 |
---|---|---|---|---|---|---|
ihOpsStac1 | NHMUK014444501 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA9065974 | SAMEA9065882 |
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope.
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 | ihOpsStac1 | 2021-07-12 | 84264 | m64089e_210712_152721 | D01 | 1015 | 3,381,911,746 | 11,361 | SAMEA9065974 |
Illumina run stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
---|---|---|---|---|---|---|---|---|---|
Chromium genome | ihOpsStac1 | 2021-07-27 | 39620_2#29 | 325,730,328 | 49,185,279,528 | SAMEA9065974 | qc complete | Opsius stactogalus (1.00) | |
Chromium genome | ihOpsStac1 | 2021-07-27 | 39620_2#32 | 358,755,554 | 54,172,088,654 | SAMEA9065974 | qc complete | Opsius stactogalus (1.00) | |
Chromium genome | ihOpsStac1 | 2021-07-27 | 39620_2#30 | 212,190,028 | 32,040,694,228 | SAMEA9065974 | qc complete | Opsius stactogalus (1.00) | |
Chromium genome | ihOpsStac1 | 2021-07-27 | 39620_2#31 | 281,002,448 | 42,431,369,648 | SAMEA9065974 | qc complete | Opsius stactogalus (1.00) |
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 |
---|---|
0.992513 | [120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...] |
0.984086 | NZ_CP013212.1 Candidatus Sulcia muelleri strain PUNC, complete genome |
0.921588 | 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 |
Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.
Features (colours represent quantile bins):
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
---|---|---|---|---|---|---|---|---|---|
No matching records found |
In-progress organelle results from MitoHiFi2.
specimen | asm | date | length | genes | frameshifts | is circular | reference |
---|---|---|---|---|---|---|---|
No matching records found |