NCBI taxon id: | 1112478 NCBI; ENA; GoaT |
---|---|
Order: | Araneae |
Family: | Scytodidae |
NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Araneae;Araneomorphae;Haplogynae;Scytodoidea;Scytodidae;Scytodes; |
GoaT genome size (M): | 2,151 (ancestor) |
GoaT asm span (M): | 3,262 (ancestor) |
GoaT chr no.: | 22 (ancestor) |
GoaT haploid no.: | 11 (ancestor) |
GoaT ploidy: | 6 (ancestor) |
ToLID prefix: | qqScyThor |
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 |
---|---|---|---|---|---|---|
qqScyThor1 | NHMUK014447002 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | CEPHALOTHORAX | SAMEA9066102 | SAMEA9066028 |
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 | qqScyThor1 | 31 | 13.56 | 360,584,249 | 64.90 | 9.19 | 58.17 | 1.99 | ![]() ![]() histogram.txt |
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 | qqScyThor1 | 2021-07-09 | 84258 | m64222e_210709_181315 | B01 | 1021 | 18,260,807,896 | 15,022 | SAMEA9066102 |
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 |
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 |
---|---|---|---|---|---|---|---|---|---|
No matching records found |
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 |
---|---|
0.918304 | 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 |
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 MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
---|---|---|---|---|---|---|---|---|
No matching records found |