Blaesoxipha plumicornis
Info
| NCBI taxon id: | 2795672 NCBI; ENA; GoaT |
|---|---|
| Order: | Diptera |
| Family: | Sarcophagidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Oestroidea;Sarcophagidae;Blaesoxipha; |
| GoaT genome size (M): | 694 (ancestor) |
| GoaT asm span (M): | 560 (ancestor) |
| GoaT chr no.: | 12 (ancestor) |
| GoaT haploid no.: | 6 (ancestor) |
| GoaT ploidy: | 3 (ancestor) |
| ToLID prefix: | idBlaPlum |
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 |
|---|---|---|---|---|---|---|
| idBlaPlum1 | Ox000781 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7746661 | SAMEA7746591 |
| idBlaPlum1 | Ox000781 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7746661 | SAMEA7746591 |
| idBlaPlum1 | Ox000781 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7746660 | SAMEA7746591 |
| idBlaPlum2 | Ox000787 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7746669 | SAMEA7746596 |
| idBlaPlum2 | Ox000787 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7746669 | SAMEA7746596 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| hic-arima2 | idBlaPlum2 | 31 | 32.52 | 879,307,151 | 67.94 | 4.72 | 97.61 | 0.47 |   histogram.txt |
| 10x | idBlaPlum1 | 31 | 26.91 | 961,819,560 | 56.96 | 3.08 | 98.08 | 0.47 |   histogram.txt |
| pacbio | idBlaPlum1 | 31 | 10.24 | 768,043,156 | 43.23 | 2.64 | 96.85 | 0.42 |   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 | idBlaPlum1 | 2021-04-10 | 81232 | m64125e_210410_152326 | B01 | 1016 | 17,953,075,872 | 16,317 | SAMEA7746661 |
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 | idBlaPlum2 | 2023-03-09 | 46860_2#5 | 547,875,460 | 82,729,194,460 | SAMEA7746669 | qc complete | Blaesoxipha plumicornis (1.00) | |
| Chromium genome | idBlaPlum1 | 2021-05-25 | 37883_1#11 | 169,941,744 | 25,661,203,344 | SAMEA7746661 | qc complete | Blaesoxipha plumicornis (1.00) | |
| Chromium genome | idBlaPlum1 | 2021-05-25 | 37883_1#9 | 140,686,136 | 21,243,606,536 | SAMEA7746661 | qc complete | Blaesoxipha plumicornis (1.00) | |
| Chromium genome | idBlaPlum1 | 2021-05-25 | 37883_1#12 | 110,582,680 | 16,697,984,680 | SAMEA7746661 | qc complete | Blaesoxipha plumicornis (1.00) | |
| Chromium genome | idBlaPlum1 | 2021-05-25 | 37883_1#10 | 123,590,262 | 18,662,129,562 | SAMEA7746661 | qc complete | Blaesoxipha plumicornis (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 |
|---|---|
| 0.974713 | [120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...] |
| 0.947187 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.917245 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.916705 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
| 0.915885 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.915608 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.912148 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.909369 | NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome |
| 0.907748 | [426 seqs] NZ_AERW01000001.1 Wolbachia endosymbiont wVitB of Nasonia vitripennis Contig_0001, whole genome shotgun sequence [...] |
| 0.906067 | [2 seqs] NC_004344.2 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis DNA, 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 |
|---|---|
| idBlaPlum1 |    |
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 | ||||||||
Tree of Life Species Report is developed within the Tree of Life Programme
at the Wellcome Sanger Institute
Copyright © 2020-2024 Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457.
Terms and conditions | Cookies policy.