Fannia serena
Info
| NCBI taxon id: | 1086765 NCBI; ENA; GoaT |
|---|---|
| Order: | Diptera |
| Family: | Fanniidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Muscoidea;Fanniidae;Fannia; |
| GoaT genome size (M): | 772 (ancestor) |
| GoaT asm span (M): | 1,337 (ancestor) |
| GoaT chr no.: | 12 (ancestor) |
| GoaT haploid no.: | 6 (ancestor) |
| GoaT ploidy: | 3 (ancestor) |
| ToLID prefix: | idFanSere |
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 |
|---|---|---|---|---|---|---|
| idFanSere1 | Ox000865 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7746830 | SAMEA7746767 |
| idFanSere2 | Ox003168 | UNIVERSITY OF OXFORD | FEMALE | WHOLE_ORGANISM | SAMEA113425929 | SAMEA113425742 |
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 | idFanSere1 | 31 | 37.15 | 41,796,482 | 90.74 | 3.27 | 86.16 | 2.54 |   histogram.txt |
| 10x | idFanSere1 | 31 | 36.59 | 285,823,864 | 96.16 | 3.17 | 86.22 | 1.54 |   histogram.txt |
| pacbio | idFanSere2 | 31 | 32.45 | 723,626 | 74.97 | 2.92 | 87.39 | 5.87 |   histogram.txt |
| hic-arima2 | idFanSere2 | 31 | 19.32 | 1,807,962,328 | 81.23 | 5.77 | 92.77 | 0.58 |   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 | idFanSere1 | 2021-04-02 | 81044 | m64230e_210402_114035 | B01 | 1020 | 6,910,774,035 | 14,860 | SAMEA7746830 | ||
| PacBio - HiFi (ULI) | idFanSere2 | 2024-07-03 | TRACTION-RUN-1361 | m84093_240703_125605_s4 | D01 | 2073 | 306,583,937 | 16,080 | SAMEA113425929 |
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 | idFanSere1 | 2021-06-01 | 37642_3#7 | 70,989,318 | 10,719,387,018 | SAMEA7746830 | qc complete | Fannia serena (1.00) | |
| Chromium genome | idFanSere1 | 2021-06-01 | 37642_3#8 | 69,661,212 | 10,518,843,012 | SAMEA7746830 | qc complete | Fannia serena (1.00) | |
| Chromium genome | idFanSere1 | 2021-06-01 | 37642_3#6 | 64,105,730 | 9,679,965,230 | SAMEA7746830 | qc complete | Fannia serena (1.00) | |
| Chromium genome | idFanSere1 | 2021-06-01 | 37642_3#5 | 103,917,132 | 15,691,486,932 | SAMEA7746830 | qc complete | Fannia serena (1.00) | |
| Hi-C - Arima v2 | idFanSere2 | 2023-10-03 | 47943_2#2 | 692,071,704 | 104,502,827,304 | SAMEA113425929 | qc complete | Fannia serena (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 |
|---|---|
| 0.989312 | [426 seqs] NZ_AERW01000001.1 Wolbachia endosymbiont wVitB of Nasonia vitripennis Contig_0001, whole genome shotgun sequence [...] |
| 0.917777 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.917245 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.915329 | [85 seqs] NZ_ATMJ01000001.1 Tatumella ptyseos ATCC 33301 contig000001, whole genome shotgun sequence [...] |
| 0.914483 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.913621 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.910933 | NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome |
| 0.910625 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.910001 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
| 0.903242 | NC_002520.1 Amsacta moorei entomopoxvirus 'L', 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 |
|---|---|
| idFanSere1 |    |
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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