Herina lugubris
Info
| NCBI taxon id: | 1335492 NCBI; ENA; GoaT |
|---|---|
| Order: | Diptera |
| Family: | Ulidiidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Tephritoidea;Herina; |
| GoaT genome size (M): | 948 (ancestor) |
| GoaT asm span (M): | 423 (ancestor) |
| GoaT chr no.: | 12 (ancestor) |
| GoaT haploid no.: | 6 (ancestor) |
| GoaT ploidy: | 3 (ancestor) |
| ToLID prefix: | idHerLugu |
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 |
|---|---|---|---|---|---|---|
| idHerLugu1 | Ox000798 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7746688 | SAMEA7746605 |
| idHerLugu2 | NHMUK014444615 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | HEAD | SAMEA7849433 | SAMEA7849380 |
| idHerLugu2 | NHMUK014444615 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | THORAX | SAMEA7849433 | SAMEA7849380 |
| idHerLugu2 | NHMUK014444615 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | ABDOMEN | SAMEA7849434 | SAMEA7849380 |
| idHerLugu3 | Ox003832 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA114645537 | SAMEA114644869 |
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 | idHerLugu1 | 31 | 9.938 | 414,634,434 | 27.17 | 1.32 | 98.95 | 0.18 |   histogram.txt |
| 10x | idHerLugu1 | 31 | 47.32 | 473,516,957 | 41.23 | 1.45 | 96.67 | 0.64 |   histogram.txt |
| hic-arima2 | idHerLugu2 | 31 | 113.7 | 396,878,560 | 30.34 | 1.09 | 97.79 | 0.38 |   histogram.txt |
| pacbio | idHerLugu3 | 31 | 81.62 | 419,322,184 | 25.57 | 1.24 | 90.76 | 0.15 |   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 | idHerLugu1 | 2021-08-15 | 85519 | m64097e_210815_044643 | C01 | 1012 | 8,739,154,736 | 11,781 | SAMEA7746688 | ||
| PacBio - HiFi | idHerLugu3 | 2024-08-15 | - | m84047_240815_105958_s4 | - | 2049 | 71,930,807,252 | 13,254 |
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 | idHerLugu1 | 2021-05-25 | 37883_3#30 | 128,597,108 | 19,418,163,308 | SAMEA7746688 | qc complete | Herina lugubris (1.00) | |
| Chromium genome | idHerLugu1 | 2021-05-25 | 37883_3#29 | 164,169,802 | 24,789,640,102 | SAMEA7746688 | qc complete | ||
| Chromium genome | idHerLugu1 | 2021-05-25 | 37883_3#31 | 98,927,564 | 14,938,062,164 | SAMEA7746688 | qc complete | Herina lugubris (1.00) | |
| Chromium genome | idHerLugu1 | 2021-05-25 | 37883_3#32 | 105,243,326 | 15,891,742,226 | SAMEA7746688 | qc complete | Herina lugubris (1.00) | |
| Hi-C - Arima v2 | idHerLugu2 | 2021-03-26 | 36940_3#4 | 839,974,534 | 126,836,154,634 | SAMEA7849433 | 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 |
|---|---|
| 0.981458 | [35 seqs] NZ_CDDI01000001.1 Aeromonas encheleia genome assembly PRJEB7027, contig F306_contig28, whole genome shotgun sequence [...] |
| 0.978386 | [92 seqs] NZ_MVON01000001.1 Acinetobacter sp. MF4642 contig001, whole genome shotgun sequence [...] |
| 0.976584 | [5 seqs] NZ_LWCN01000001.1 Delftia sp. GW456-R20 scaffold1, whole genome shotgun sequence [...] |
| 0.968984 | [5 seqs] NZ_KB976071.1 Citrobacter sp. KTE32 acHXe-supercont1.1, whole genome shotgun sequence [...] |
| 0.968535 | [344 seqs] NZ_ASZT02000001.1 Sphingobacterium sp. IITKGP-BTPF85 Sphingobacterium_sp_IITKGP-BTPF85_Contig_00001, whole genome shotgun sequence [...] |
| 0.961556 | NZ_CP012608.1 Acinetobacter sp. TTH0-4, complete genome |
| 0.956962 | [30 seqs] NZ_LMED01000001.1 Acinetobacter sp. Root1280 contig_1, whole genome shotgun sequence [...] |
| 0.93855 | [8 seqs] NZ_KB849702.1 Acinetobacter johnsonii ANC 3681 genomic scaffold acLro-supercont1.1, whole genome shotgun sequence [...] |
| 0.937001 | [72 seqs] NZ_FUZE01000069.1 Chryseobacterium balustinum strain DSM 16775, whole genome shotgun sequence [...] |
| 0.921831 | 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 |
|---|---|
| idHerLugu1 |    |
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 | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
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