Bombus hypnorum
Tree bumblebee
Info
| NCBI taxon id: | 30191 NCBI; ENA; GoaT |
|---|---|
| Order: | Hymenoptera |
| Family: | Apidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Hymenoptera;Apocrita;Aculeata;Apoidea;Anthophila;Apidae;Bombus;Pyrobombus; |
| GoaT genome size (M): | 408 (ancestor) |
| GoaT asm span (M): | 297 (direct) |
| GoaT chr no.: | 36 (ancestor) |
| GoaT haploid no.: | 18 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | iyBomHypn |
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 |
|---|---|---|---|---|---|---|
| iyBomHypn1 | Ox000434 | UNIVERSITY OF OXFORD | MALE | ABDOMEN | SAMEA7520731 | SAMEA7520655 |
| iyBomHypn1 | Ox000434 | UNIVERSITY OF OXFORD | MALE | THORAX | SAMEA7520730 | SAMEA7520655 |
| iyBomHypn1 | Ox000434 | UNIVERSITY OF OXFORD | MALE | HEAD | SAMEA7520730 | SAMEA7520655 |
| iyBomHypn2 | NHMUK014111095 | NATURAL HISTORY MUSEUM | FEMALE | THORAX | SAMEA7521615 | SAMEA7521526 |
| iyBomHypn2 | NHMUK014111095 | NATURAL HISTORY MUSEUM | FEMALE | THORAX | SAMEA7521614 | SAMEA7521526 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 10x | iyBomHypn1 | 31 | 31.78 | 426,866,271 | 44.78 | 0.02 | 97.24 | 0.51 |   histogram.txt |
| pacbio | iyBomHypn1 | 31 | 16.64 | 332,128,708 | 29.07 | 0.06 | 99.09 | 0.15 |   histogram.txt |
| hic-arima2 | iyBomHypn1 | 31 | 160.3 | 299,695,636 | 98.35 | 18.60 | 95.34 | 0.41 |   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 | iyBomHypn1 | 2020-09-10 | 77367 | m64125_200910_151800 | A01 | 1011 | 11,616,206,786 | 11,418 | SAMEA7520730 | ERR6412371 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | iyBomHypn1 | 2020-10-27 | 35278_8#3 | 58,889,650 | 8,892,337,150 | SAMEA7520730 | ERR6054789 | qc complete | Bombus hypnorum (1.00) |
| Chromium genome | iyBomHypn1 | 2020-10-27 | 35278_8#1 | 94,888,134 | 14,328,108,234 | SAMEA7520730 | ERR6054787 | qc complete | Bombus hypnorum (1.00) |
| Chromium genome | iyBomHypn1 | 2020-10-27 | 35278_8#4 | 63,970,054 | 9,659,478,154 | SAMEA7520730 | ERR6054790 | qc complete | Bombus hypnorum (1.00) |
| Chromium genome | iyBomHypn1 | 2020-10-27 | 35278_8#2 | 72,523,592 | 10,951,062,392 | SAMEA7520730 | ERR6054788 | qc complete | Bombus hypnorum (1.00) |
| Hi-C - Arima v2 | iyBomHypn1 | 2020-10-02 | 35140_2#1 | 901,228,034 | 136,085,433,134 | SAMEA7520730 | ERR6054786 | qc complete | Bombus hypnorum (1.00) |
| RNA PolyA | iyBomHypn2 | 2021-05-25 | 37935_6#13 | 53,615,830 | 8,095,990,330 | SAMEA7521615 | ERR6363265 | qc complete | Bombus hypnorum (1.00) |
| RNA PolyA | iyBomHypn2 | 2021-05-25 | 37935_5#6 | 37,368,430 | 5,642,632,930 | SAMEA7521615 | ERR6363264 | qc complete | Bombus hypnorum (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 |
|---|---|
| 0.974154 | [5559 seqs] NT_176420.1 Bombus impatiens unplaced genomic scaffold, BIMP_2.0 scf_0001, whole genome shotgun sequence [...] |
| 0.903605 | 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 |
|---|---|
| iyBomHypn1 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| iyBomHypn1 | hifiasm.purging | 2020-10-15 | 11,976,358 | 55 | 284,032,711 | C:99.8%[S:99.3%,D:0.5%],F:0.1%,M:0.1%,n:1658 | - | ||
| iyBomHypn1 | hifiasm.scaff.salsa | 2020-10-15 | 11,840,314 | 68 | 12,287,591 | 54 | 284,038,345 | - | |
| iyBomHypn1 | hifiasm | 2020-10-15 | 10,909,865 | 446 | 356,023,499 | C:99.8%[S:99.3%,D:0.5%],F:0.1%,M:0.1%,n:1658 | - | ||
| iyBomHypn1 | hicanu | 2020-10-15 | 6,399,562 | 1,701 | 420,535,120 | C:99.6%[S:98.0%,D:1.6%],F:0.2%,M:0.2%,n:1658 | - | ||
| iyBomHypn1 | hicanu.purging | 2020-10-15 | 11,979,552 | 77 | 276,936,002 | C:99.6%[S:99.1%,D:0.5%],F:0.2%,M:0.2%,n:1658 | - | ||
| iyBomHypn1 | hicanu.scaff.salsa | 2020-10-15 | 11,979,507 | 87 | 12,286,737 | 76 | 276,939,916 | - |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| iyBomHypn1 | mitohifi.reads | mito | 2020-10-15 | 15,443 | 26 | None | False | LC702705.1; 15,793 bp; 38 genes |
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