Aponogeton distachyos
Info
| NCBI taxon id: | 55311 NCBI; ENA; GoaT |
|---|---|
| Order: | Alismatales |
| Family: | Aponogetonaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;Liliopsida;Aponogetonaceae;Aponogeton; |
| GoaT genome size (M): | unknown (unknown) |
| GoaT asm span (M): | unknown (unknown) |
| GoaT chr no.: | unknown (unknown) |
| GoaT haploid no.: | unknown (unknown) |
| GoaT ploidy: | unknown (unknown) |
| ToLID prefix: |
Specimens
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
Loading, please wait
tolid | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| laApoDist1 | KDTOL10071 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522371 | SAMEA7522292 |
| laApoDist1 | KDTOL10071 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | STEM | SAMEA7522367 | SAMEA7522292 |
| laApoDist1 | KDTOL10071 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522369 | SAMEA7522292 |
| laApoDist1 | KDTOL10071 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522370 | SAMEA7522292 |
| laApoDist1 | KDTOL10071 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522372 | SAMEA7522292 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.
Loading, please wait
source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| pacbio | laApoDist1 | 31 | 31.12 | 4,556,390,483 | 76.17 | 0.34 | 94.21 | 0.10 |   histogram.txt |
| hic-arima2 | laApoDist1 | 31 | 5.142 | 72,451,050,997 | 0.00 | 100.00 | 7.33 | 0.18 |   histogram.txt |
Sequence data
PacBio run data
Below are stats for each PacBio seqeuncing run collected for this species.
Loading, please wait
pipeline | specimen | date | run id | movie | well | tag | yield | N50 | sample accession | run accession | barcode |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PacBio - HiFi | laApoDist1 | 2021-02-18 | 79913 | m64174e_210218_160858 | A01 | 1020 | 3,786,433,331 | 15,320 | SAMEA7522368 | ||
| PacBio - HiFi (ULI) | laApoDist1 | 2023-05-15 | TRACTION-RUN-588 | m64178e_230515_223511 | D01 | 1010 | 21,655,277,010 | 8,731 | SAMEA7522371 | ||
| PacBio - HiFi | laApoDist1 | 2023-06-20 | TRACTION-RUN-645 | m84047_230620_130731_s3 | C01 | 2035 | 58,467,449,590 | 15,418 | SAMEA7522371 | ||
| PacBio - HiFi | laApoDist1 | 2023-07-07 | TRACTION-RUN-670 | m84047_230707_160909_s1 | C01 | 2022 | 24,712,446,566 | 17,468 | SAMEA7522371 | ||
| PacBio - HiFi | laApoDist1 | 2023-09-29 | TRACTION-RUN-861 | m84047_230929_150655_s3 | C01 | 2035 | 62,626,116,846 | 15,781 | SAMEA7522371 | ||
| PacBio - HiFi | laApoDist1 | 2023-12-08 | TRACTION-RUN-992 | m84093_231208_110757_s1 | A01 | 2006 | 34,872,648,744 | 14,303 | SAMEA10369677 | ||
| PacBio - HiFi | laApoDist1 | 2023-12-09 | TRACTION-RUN-993 | m84098_231209_111237_s1 | A01 | 2002 | 87,130,233,531 | 16,274 | SAMEA10369677 |
Showing 1 to 7 of 7 rows
ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
Loading, please wait
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.
Loading, please wait
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Hi-C - Arima v2 | laApoDist1 | 2022-09-16 | 45817_2#1 | 6,508,838,724 | 982,834,647,324 | SAMEA7522371 | qc complete | Aponogeton distachyos (1.00) |
Showing 1 to 1 of 1 rows
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.
Loading, please wait
identity | info |
|---|---|
| 0.943372 | [84 seqs] NZ_BBJS01000082.2 Sphingomonas paucimobilis NBRC 13935 DNA, contig: SP682, whole genome shotgun sequence [...] |
| 0.942757 | [151 seqs] NZ_JICM01000001.1 Acinetobacter sp. ETR1 contig_1, whole genome shotgun sequence [...] |
| 0.923964 | [58 seqs] NZ_ATUI01000001.1 Rubrivivax benzoatilyticus JA2 = ATCC BAA-35 strain JA2 F799DRAFT_scaffold00001.1_C, whole genome shotgun sequence [...] |
| 0.920352 | [30 seqs] NZ_LNIU01000001.1 Rhodococcus equi strain MET contig_10, whole genome shotgun sequence [...] |
| 0.918565 | [16 seqs] NZ_KB849280.1 Acinetobacter guillouiae CIP 63.46 genomic scaffold acLsj-supercont1.1, whole genome shotgun sequence [...] |
| 0.917512 | NZ_AP012549.1 Cyanobacterium endosymbiont of Epithemia turgida isolate EtSB Lake Yunoko DNA, complete genome |
| 0.91616 | [58 seqs] NZ_LZQD01000001.1 Trichormus sp. NMC-1 scaffold1, whole genome shotgun sequence [...] |
| 0.912446 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.906747 | [58 seqs] NZ_ATUI01000001.1 Rubrivivax benzoatilyticus JA2 = ATCC BAA-35 strain JA2 F799DRAFT_scaffold00001.1_C, whole genome shotgun sequence [...] |
| 0.905724 | NZ_CM001438.1 Burkholderiales bacterium JOSHI_001 chromosome, whole genome shotgun sequence |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
Loading, please wait
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| laApoDist1_homcov62 | atg000004l | 1806 |
|
| laApoDist1 | atg000005l | 1806 |
|
| laApoDist1 | atg000009l | 1806 |
|
| laApoDist1 | atg000020l | 1807 |
|
| laApoDist1_homcov62 | atg000073l | 1463 |
|
| laApoDist1_homcov62 | atg000075l | 1802 |
|
| laApoDist1_homcov62 | atg000078l | 1780 |
|
| laApoDist1 | atg000079l | 1806 |
|
| laApoDist1 | atg000083l | 1463 |
|
| laApoDist1 | atg000085l | 1802 |
|
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.
Loading, please wait
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.
Loading, please wait
specimen | visualisation |
|---|---|
| laApoDist1 |    |
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
laApoDist1.hifiasm.20240108
Assemblies
In-progress assembly QC.
Loading, please wait
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| laApoDist1_homcov62 | hifiasm | 2024-06-14 | 13,071,170 | 5,856 | 4,821,209,368 | C:98.8%[S:90.1%,D:8.7%],F:0.7%,M:0.5%,n:425 | Q59.9-C98.0(HiFi) | ||
| laApoDist1 | hifiasm.purging | 2024-01-08 | 14,659,316 | 1,943 | 3,679,310,562 | C:89.6%[S:81.6%,D:8.0%],F:1.9%,M:8.5%,n:425 | Q62.2-C84.8(HiFi) | ||
| laApoDist1 | hifiasm.scaffolding.yahs | 2024-01-08 | 9,573,982 | 2,523 | 168,211,681 | 1,492 | 3,679,516,762 | C:89.6%[S:82.1%,D:7.5%],F:1.9%,M:8.5%,n:425 | Q62.2-C84.8(HiFi) |
| laApoDist1 | hifiasm | 2024-01-08 | 14,014,291 | 5,438 | 4,550,066,198 | C:98.9%[S:90.4%,D:8.5%],F:0.7%,M:0.4%,n:425 | Q59.7-C97.8(HiFi) | ||
| laApoDist1 | hifiasm-hic.purging | 2024-01-08 | 9,811,707 | 2,289 | 3,542,808,440 | C:88.9%[S:79.5%,D:9.4%],F:1.4%,M:9.7%,n:425 | Q62.4-C83.2(HiFi) | ||
| laApoDist1 | hifiasm-hic.scaffolding.yahs | 2024-01-08 | 7,810,000 | 2,782 | 158,596,167 | 1,564 | 3,543,052,040 | C:88.9%[S:80.0%,D:8.9%],F:1.4%,M:9.7%,n:425 | Q62.4-C83.2(HiFi) |
| laApoDist1 | hifiasm-hic.hap2 | 2024-01-08 | 4,697,979 | 1,782 | 1,683,684,816 | C:48.0%[S:38.1%,D:9.9%],F:3.3%,M:48.7%,n:425 | - | ||
| laApoDist1 | hifiasm-hic.hap1 | 2024-01-08 | 8,840,111 | 6,170 | 4,189,296,947 | C:93.4%[S:83.5%,D:9.9%],F:1.2%,M:5.4%,n:425 | Q59.7-C97.8(HiFi) | ||
| laApoDist1_homcov62 | hifiasm-hic.hap2 | 2024-06-14 | 10,846,022 | 2,715 | 4,587,129,010 | C:98.6%[S:91.1%,D:7.5%],F:0.7%,M:0.7%,n:425 | Q63.8-C98.0(HiFi) | ||
| laApoDist1_homcov62 | hifiasm-hic.hap1 | 2024-06-14 | 10,466,097 | 5,393 | 4,652,358,525 | C:98.3%[S:89.4%,D:8.9%],F:0.7%,M:1.0%,n:425 | Q60.5-C98.0(HiFi) | ||
| laApoDist1_homcov62 | hifiasm-hic.scaffolding_hap1.yahs | 2024-06-14 | 7,839,000 | 6,331 | 223,618,302 | 5,140 | 4,652,596,725 | C:98.4%[S:89.9%,D:8.5%],F:0.7%,M:0.9%,n:425 | Q60.5-C98.0(HiFi) |
| laApoDist1_homcov62 | hifiasm-hic.scaffolding_hap2.yahs | 2024-06-14 | 7,799,266 | 3,650 | 220,591,749 | 2,534 | 4,587,352,210 | C:98.9%[S:91.8%,D:7.1%],F:0.7%,M:0.4%,n:425 | Q63.8-C98.0(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
Loading, please wait
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| laApoDist1_homcov62 | oatk.reads | pltd | 2024-06-14 | 153,518 | 108 | rps2 | True | 1 | NC_053914.1; 154,167 bp; 130 genes |
| laApoDist1_homcov62 | oatk.reads | mito | 2024-06-14 | 231,091 | 46 | None | True | 1 | NC_088727.1; 256,174 bp; 44 genes |
| laApoDist1 | oatk.reads | pltd | 2024-01-08 | 153,518 | 108 | rps2 | True | 1 | NC_053914.1; 154,167 bp; 130 genes |
| laApoDist1 | oatk.reads | mito | 2024-01-08 | 231,091 | 49 | ND1 | True | 1 | OQ948332.1; 876,608 bp; 61 genes |
Tree of Life Species Report is developed within the Tree of Life Programme
at the Wellcome Sanger Institute
Copyright © 2020-2024 Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457.
Terms and conditions | Cookies policy.