Calvia quattuordecimguttata
cream-spotted lady beetle
Info
| NCBI taxon id: | 419956 NCBI; ENA; GoaT |
|---|---|
| Order: | Coleoptera |
| Family: | Coccinellidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Coleoptera;Polyphaga;Cucujiformia;Coccinelloidea;Coccinellidae;Coccinellinae;Coccinellini;Calvia; |
| GoaT genome size (M): | 403 (ancestor) |
| GoaT asm span (M): | 482 (ancestor) |
| GoaT chr no.: | 20 (direct) |
| GoaT haploid no.: | 10 (direct) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | icCalQuat |
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 |
|---|---|---|---|---|---|---|
| icCalQuat1 | Ox000117 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7520291 | SAMEA7520199 |
| icCalQuat2 | Ox000329 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA8603306 | SAMEA8563703 |
| icCalQuat3 | NHMUK014439779 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | THORAX | SAMEA14448733 | SAMEA14448390 |
| icCalQuat3 | NHMUK014439779 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | HEAD | SAMEA14448733 | SAMEA14448390 |
| icCalQuat3 | NHMUK014439779 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | ABDOMEN | SAMEA14448732 | SAMEA14448390 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| pacbio | icCalQuat2 | 31 | 21.61 | 425,271,970 | 51.96 | 87.32 | 87.02 | 0.81 |   histogram.txt |
| hic-arima2 | icCalQuat3 | 31 | 65.21 | 829,381,294 | 67.33 | 4.29 | 96.70 | 0.40 |   histogram.txt |
| pacbio | icCalQuat4 | 31 | 13.78 | 863,278,997 | 51.69 | 1.93 | 97.93 | 0.14 |   histogram.txt |
| pacbio | icCalQuat1 | 31 | 37.31 | 20,228,227 | 85.27 | 3.25 | 86.61 | 3.21 |   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 | icCalQuat1 | 2020-05-21 | TRACTION-RUN-35 | m64097_200521_140146 | A01 | 1012 | 4,160,847,814 | 14,842 | SAMEA7520291 | ||
| PacBio - HiFi | icCalQuat2 | 2022-11-19 | TRACTION-RUN-343 | m64229e_221119_193220 | C01 | 1021 | 23,688,862,914 | 15,629 | SAMEA8603306 | ||
| PacBio - HiFi | icCalQuat4 | 2024-03-21 | TRACTION-RUN-1197 | m64178e_240321_195434 | B01 | 2058 | 24,892,069,073 | 11,624 | SAMEA14448746 |
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 | icCalQuat3 | 2023-01-09 | 46359_4#4 | 1,013,668,098 | 153,063,882,798 | SAMEA14448733 | qc complete | Calvia quatuordecimguttata (1.00) | |
| RNA PolyA | icCalQuat5 | 2023-08-03 | 47585_1#58 | 62,030,072 | 9,366,540,872 | SAMEA111458477 | qc complete | Calvia quatuordecimguttata (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 |
|---|---|
| 0.944728 | [22 seqs] NZ_KI440934.1 Pantoea agglomerans Tx10 scaffold134, whole genome shotgun sequence [...] |
| 0.909049 | 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 |
|---|---|---|---|
| icCalQuat4 | atg000097l | 1496 |
|
| icCalQuat4 | atg001729l | 1904 |
|
| icCalQuat4 | ptg000042l | 970 |
|
| icCalQuat4 | ptg000088l | 1538 |
|
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 | ||
| icCalQuat4 | Erwiniaceae | 7,679 | 0.3 | C:96.6%[S:8.6%,D:88.0%],F:3.2%,M:0.2%,n:440 | C:73.2%[S:72.7%,D:0.5%],F:20.5%,M:6.3%,n:440 | 4 | 5.41Mb | 7,312 | C:73.1%[S:72.0%,D:1.1%],F:20.5%,M:6.4%,n:440 | 5 | 5.43Mb | 7,435 |
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| icCalQuat1 |    |
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
icCalQuat4.hifiasm.20240327
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| icCalQuat4 | hifiasm | 2024-03-27 | 14,499,845 | 341 | 928,275,487 | C:99.0%[S:95.0%,D:4.0%],F:0.1%,M:0.9%,n:1367 | Q64.8-C98.8(HiFi) | ||
| icCalQuat4 | hifiasm.scaffolding_alt.yahs | 2024-03-27 | 3,272,153 | 2,614 | 40,346,767 | 2,115 | 942,392,175 | C:98.8%[S:96.3%,D:2.5%],F:0.4%,M:0.8%,n:1367 | Q64.9-C98.8(HiFi) |
| icCalQuat4 | hifiasm.purging | 2024-03-27 | 16,077,089 | 130 | 833,332,233 | C:98.8%[S:96.8%,D:2.0%],F:0.1%,M:1.1%,n:1367 | Q66.2-C98.3(HiFi) | ||
| icCalQuat4 | hifiasm.scaffolding.yahs | 2024-03-27 | 14,945,000 | 151 | 49,444,229 | 73 | 833,347,833 | C:98.9%[S:96.9%,D:2.0%],F:0.1%,M:1.0%,n:1367 | Q66.2-C98.3(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| icCalQuat4 | mitohifi.hifiasm | mito | 2024-03-27 | 19,446 | 37 | None | True | 1 | NC_058236.1; 17,630 bp; 37 genes |
| icCalQuat4 | mitohifi.reads | mito | 2024-03-27 | 19,446 | 37 | None | True | 1 | NC_058236.1; 17,630 bp; 37 genes |
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