Myodes glareolus
Bank vole
Info
| NCBI taxon id: | 447135 |
|---|---|
| Order: | Rodentia |
| Family: | Cricetidae |
| NCBI lineage: | Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Euarchontoglires;Glires;Rodentia;Myomorpha;Muroidea;Cricetidae;Arvicolinae;Myodes; |
| GoaT genome size (M): | 2,748 (direct) |
| GoaT asm span (M): | 2,359 (direct) |
| GoaT chr no.: | 56 (direct) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | mMyoGla |
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 |
|---|---|---|---|---|---|---|
| mMyoGla1 | Ox000986 | UNIVERSITY OF OXFORD | FEMALE | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA7702032 | SAMEA7702027 |
| mMyoGla2 | Ox000987 | UNIVERSITY OF OXFORD | MALE | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA7702033 | SAMEA7702028 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 10x | mMyoGla1 | 31 | 18.63 | 2,740,899,116 | 22.56 | 0.36 | 99.23 | 0.43 |   |
| pacbio | mMyoGla1 | 31 | 9.597 | 2,574,862,949 | 16.55 | 0.42 | 99.77 | 0.16 |   |
| hic-arima2 | mMyoGla2 | 31 | 78.48 | 2,323,493,261 | 15.70 | 1.08 | 96.78 | 0.42 |   |
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 | mMyoGla1 | 2021-03-20 | 80685 | m64097e_210320_151727 | C01 | 1022 | 22,363,262,836 | 11,395 | SAMEA7702032 | ||
| PacBio - HiFi | mMyoGla1 | 2021-04-11 | 81230 | m64221e_210411_150122 | C01 | 1022 | 12,998,802,516 | 12,487 | SAMEA7702032 | ||
| PacBio - HiFi | mMyoGla1 | 2021-04-12 | 81230 | m64221e_210412_152303 | D01 | 1022 | 16,679,937,526 | 11,877 | SAMEA7702032 |
Illumina run data
Illumina run stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | mMyoGla1 | 2021-04-08 | 37177_3#21 | 261,155,180 | 39,434,432,180 | SAMEA7702032 | qc complete | Myodes glareolus (1.00) | |
| Chromium genome | mMyoGla1 | 2021-04-08 | 37177_3#24 | 254,205,120 | 38,384,973,120 | SAMEA7702032 | qc complete | Myodes glareolus (1.00) | |
| Chromium genome | mMyoGla1 | 2021-04-08 | 37177_3#23 | 254,526,418 | 38,433,489,118 | SAMEA7702032 | qc complete | Myodes glareolus (1.00) | |
| Chromium genome | mMyoGla1 | 2021-04-08 | 37177_3#22 | 290,385,088 | 43,848,148,288 | SAMEA7702032 | qc complete | Myodes glareolus (1.00) | |
| Hi-C - Arima v2 | mMyoGla2 | 2021-08-16 | 40063_2#1 | 3,425,113,950 | 517,192,206,450 | SAMEA7702033 | qc complete | Myodes glareolus (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 |
|---|---|
| 0.930838 | [6335 seqs] NC_022009.1 Microtus ochrogaster isolate Prairie Vole_2 chromosome 1, MicOch1.0, whole genome shotgun sequence [...] |
| 0.925333 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.906747 | [66 seqs] NZ_JACX01000001.1 Bartonella grahamii ATCC 700132 U736DRAFT_scaffold00001.1_C, whole genome shotgun sequence [...] |
| 0.902507 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.902507 | [777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...] |
| 0.900986 | NC_021929.1 Malvastrum leaf curl Philippines betasatellite, complete sequence |
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 |
|---|---|
| mMyoGla1 |    |
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 | ||||||||
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