Buathra laborator
Info
| NCBI taxon id: | 1419289 NCBI; ENA; GoaT |
|---|---|
| Order: | Hymenoptera |
| Family: | Ichneumonidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Hymenoptera;Apocrita;Ichneumonoidea;Ichneumonidae;Cryptinae;Cryptina;Buathra; |
| GoaT genome size (M): | 264 (ancestor) |
| GoaT asm span (M): | 329 (direct) |
| GoaT chr no.: | 22 (ancestor) |
| GoaT haploid no.: | 10 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | iyBuaLabo |
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 |
|---|---|---|---|---|---|---|
| iyBuaLabo1 | NHMUK014444523 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | THORAX | SAMEA8534307 | SAMEA8534297 |
| iyBuaLabo1 | NHMUK014444523 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | ABDOMEN | SAMEA8534306 | SAMEA8534297 |
| iyBuaLabo1 | NHMUK014444523 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | HEAD | SAMEA8534305 | SAMEA8534297 |
| iyBuaLabo2 | NHMUK014536808 | NATURAL HISTORY MUSEUM | MALE | ABDOMEN | SAMEA112221941 | SAMEA112221843 |
| iyBuaLabo2 | NHMUK014536808 | NATURAL HISTORY MUSEUM | MALE | ABDOMEN | SAMEA112222102 | SAMEA112221843 |
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 | iyBuaLabo1 | 31 | 59.73 | 344,032,074 | 49.10 | 0.81 | 97.31 | 0.69 |   histogram.txt |
| pacbio | iyBuaLabo1 | 31 | 24.44 | 277,118,207 | 33.34 | 0.70 | 98.14 | 0.19 |   histogram.txt |
| hic-arima2 | iyBuaLabo1 | 31 | 117.7 | 387,755,549 | 68.10 | 1.24 | 98.90 | 0.38 |   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 | iyBuaLabo1 | 2021-05-10 | 82093 | m64016e_210510_045933 | C01 | 1009 | 14,421,052,167 | 15,098 | SAMEA8534307 | ERR8482057 |
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 | iyBuaLabo1 | 2021-05-26 | 38128_4#16 | 112,086,666 | 16,925,086,566 | SAMEA8534307 | ERR8373783 | qc complete | |
| Chromium genome | iyBuaLabo1 | 2021-05-26 | 38128_4#13 | 107,249,898 | 16,194,734,598 | SAMEA8534307 | ERR8373780 | qc complete | Buathra laborator (1.00) |
| Chromium genome | iyBuaLabo1 | 2021-05-26 | 38128_4#15 | 122,346,224 | 18,474,279,824 | SAMEA8534307 | ERR8373782 | qc complete | |
| Chromium genome | iyBuaLabo1 | 2021-05-26 | 38128_4#14 | 120,464,066 | 18,190,073,966 | SAMEA8534307 | ERR8373781 | qc complete | Buathra laborator (1.00) |
| Hi-C - Arima v2 | iyBuaLabo1 | 2021-10-05 | 41252_2#3 | 844,841,854 | 127,571,119,954 | SAMEA8534305 | ERR8373784 | qc complete |
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 |
|---|---|
| 0.91616 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.909369 | [22 seqs] NZ_KI440934.1 Pantoea agglomerans Tx10 scaffold134, whole genome shotgun sequence [...] |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| iyBuaLabo1 | atg000419l | 1013 |
|
| iyBuaLabo1 | ptg000233l | 1913 |
|
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 |
|---|---|
| iyBuaLabo1 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| iyBuaLabo1 | hicanu | 2021-10-05 | 2,082,735 | 3,671 | 699,122,856 | C:99.7%[S:55.1%,D:44.6%],F:0.0%,M:0.3%,n:1367 | Q41.5-C94.3(10X); Q67.7-C99.4(HiFi) | ||
| iyBuaLabo1 | hicanu.purging | 2021-10-05 | 8,438,396 | 375 | 310,870,389 | C:99.4%[S:99.0%,D:0.4%],F:0.1%,M:0.5%,n:1367 | Q54.1-C94.2(10X); Q69.5-C99.2(HiFi) | ||
| iyBuaLabo1 | hifiasm.purging | 2021-10-05 | 10,417,793 | 138 | 329,945,213 | C:99.6%[S:99.2%,D:0.4%],F:0.1%,M:0.3%,n:1367 | Q57.7-C94.2(10X); Q64.2-C99.1(HiFi) | ||
| iyBuaLabo1 | hifiasm.scaff.salsa | 2021-10-05 | 10,417,199 | 142 | 12,772,607 | 129 | 329,933,837 | - | |
| iyBuaLabo1 | hifiasm | 2021-10-05 | 7,977,642 | 370 | 359,101,690 | C:99.6%[S:99.2%,D:0.4%],F:0.1%,M:0.3%,n:1367 | Q54.5-C94.3(10X); Q62.2-C99.3(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| iyBuaLabo1 | mitohifi.hicanu | mito | 2021-10-05 | 40,260 | 37 | None | EU871947.1; 18,728 bp; 37 genes | |
| iyBuaLabo1 | mitohifi.reads | mito | 2021-10-05 | 35,155 | 40 | None | EU871947.1; 18,728 bp; 37 genes | |
| iyBuaLabo1 | mitohifi.hifiasm | mito | 2021-10-05 | 35,843 | 40 | None | EU871947.1; 18,728 bp; 37 genes |
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