Parietaria judaica
Info
| NCBI taxon id: | 33127 NCBI; ENA; GoaT |
|---|---|
| Order: | Rosales |
| Family: | Urticaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Urticaceae;Parietaria; |
| GoaT genome size (M): | 753 (direct) |
| GoaT asm span (M): | 538 (direct) |
| GoaT chr no.: | 26 (direct) |
| GoaT haploid no.: | 7 (direct) |
| GoaT ploidy: | 2 (direct) |
| ToLID prefix: | drParJuda |
Specimens
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
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tolid | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| drParJuda1 | KDTOL10061 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522281 | SAMEA7522182 |
| drParJuda1 | KDTOL10061 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522280 | SAMEA7522182 |
| drParJuda1 | KDTOL10061 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522297 | SAMEA7522182 |
| drParJuda1 | KDTOL10061 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522299 | SAMEA7522182 |
| drParJuda1 | KDTOL10061 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522298 | SAMEA7522182 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.
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source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| 10x | drParJuda1 | 31 | 61.47 | 351,621,425 | 55.64 | 10.85 | 92.08 | 0.46 |   histogram.txt |
| pacbio | drParJuda1 | 31 | 28.54 | 302,028,896 | 49.74 | 9.81 | 93.30 | 0.26 |   histogram.txt |
| hic-arima2 | drParJuda1 | 31 | 55.93 | 772,981,186 | 0.00 | 1.97 | 0.75 | 0.21 |   histogram.txt |
Sequence data
PacBio run data
Below are stats for each PacBio seqeuncing run collected for this species.
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pipeline | specimen | date | run id | movie | well | tag | yield | N50 | sample accession | run accession | barcode |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PacBio - HiFi | drParJuda1 | 2021-04-26 | 81618 | m64097e_210426_091413 | D01 | 1011 | 10,243,241,930 | 14,890 | SAMEA7522280 | ERR9709341 | |
| PacBio - HiFi | drParJuda1 | 2021-07-29 | 85020 | m64221e_210729_121644 | A01 | 1011 | 8,474,889,006 | 13,856 | SAMEA7522280 | ERR9709342 |
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ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
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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.
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pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | drParJuda1 | 2021-03-25 | 37020_4#7 | 87,389,488 | 13,195,812,688 | SAMEA7522280 | ERR9710926 | qc complete | Parietaria judaica (1.00) |
| Chromium genome | drParJuda1 | 2021-03-25 | 37020_4#6 | 118,673,406 | 17,919,684,306 | SAMEA7522280 | ERR9710925 | qc complete | Parietaria judaica (1.00) |
| Chromium genome | drParJuda1 | 2021-03-25 | 37020_4#8 | 116,310,232 | 17,562,845,032 | SAMEA7522280 | ERR9710927 | qc complete | Parietaria judaica (1.00) |
| Chromium genome | drParJuda1 | 2021-03-25 | 37020_4#5 | 132,604,590 | 20,023,293,090 | SAMEA7522280 | ERR9710924 | qc complete | Parietaria judaica (1.00) |
| Hi-C - Arima v2 | drParJuda1 | 2021-12-09 | 42130_4#6 | 761,993,926 | 115,061,082,826 | SAMEA7522299 | ERR9710928 | qc complete | Parietaria judaica (1.00) |
| RNA PolyA | drParJuda1 | 2023-06-22 | 47503_1#3 | 75,361,550 | 11,379,594,050 | SAMEA7522297 | ERR11641095 | qc complete | Parietaria judaica (1.00) |
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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.
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identity | info |
|---|---|
| 0.91934 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
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Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
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specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| drParJuda1 | atg000677l | 1192 |
|
| drParJuda1 | atg003820l | 1823 |
|
| drParJuda1 | ptg000018l | 589 |
|
| drParJuda1 | ptg000033l | 1805 |
|
| drParJuda1 | ptg000112l | 604 |
|
| drParJuda1 | ptg000200l | 1488 |
|
| drParJuda1 | ptg000339l | 1109 |
|
| drParJuda1 | ptg000429l | 827 |
|
| drParJuda1 | ptg000510l | 1798 |
|
| drParJuda1 | ptg000523l | 823 |
|
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.
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specimen | family | classified reads | original assembly | re-assembly | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | number of reads | BUSCO | contigs | contig length | number of reads | ||
| drParJuda1 | Cladosporiaceae | 2,253 | 0.01 | - | - | 1 | 0.02Mb | 32 | - | 0.00Mb | ||
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Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
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specimen | visualisation |
|---|---|
| drParJuda1 |    |
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
BTK datasets:
Assemblies
In-progress assembly QC.
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specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| drParJuda1 | hicanu.purging | 2021-12-14 | 10,442,385 | 360 | 536,391,435 | C:95.8%[S:13.5%,D:82.3%],F:0.7%,M:3.5%,n:2326 | Q53.1-C95.9(10X); Q60.4-C98.8(HiFi) | ||
| drParJuda1 | hicanu | 2021-12-14 | 3,731,754 | 8,734 | 939,818,695 | C:95.9%[S:4.0%,D:91.9%],F:0.7%,M:3.4%,n:2326 | Q39.2-C96.5(10X); Q61.1-C99.4(HiFi) | ||
| drParJuda1 | hifiasm.cutadapt.all.overlap12 | 2022-11-23 | 7,843,770 | 738 | 645,911,977 | - | |||
| drParJuda1 | hifiasm.cutadapt | 2022-11-23 | 7,843,770 | 744 | 646,348,182 | - | |||
| drParJuda1 | hifiasm.cutadapt | 2022-11-23 | 5,010,245 | 964 | 566,814,158 | - | |||
| drParJuda1 | hifiasm.cutadapt.bc1011 | 2022-11-23 | 7,567,283 | 923 | 567,671,010 | - | |||
| drParJuda1 | hifiasm | 2022-11-23 | 23,971,113 | 679 | 646,122,316 | - | |||
| drParJuda1 | hifiasm.purging | 2021-12-14 | 18,710,002 | 148 | 540,921,109 | C:95.7%[S:12.3%,D:83.4%],F:0.8%,M:3.5%,n:2326 | Q52.8-C95.7(10X); Q60.3-C98.6(HiFi) | ||
| drParJuda1 | hifiasm.scaff.yahs | 2021-12-14 | 16,564,159 | 156 | 39,878,902 | 121 | 540,922,528 | - | |
| drParJuda1 | hifiasm | 2021-12-14 | 15,268,960 | 898 | 630,640,449 | C:95.7%[S:5.4%,D:90.3%],F:0.7%,M:3.6%,n:2326 | Q48.4-C96.3(10X); Q58.2-C99.1(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
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specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| drParJuda1 | oatk.reads | mito | 2021-12-14 | 222,342 | 36 | rps10;atp9 | False | ON930432.1; 415,837 bp; 54 genes |
| drParJuda1 | oatk.reads | pltd | 2021-12-14 | 152,629 | 107 | rps16;atpF | True | NC_066035.1; 152,689 bp; 130 genes |
| drParJuda1 | oatk.reads | mito | 2021-12-14 | 222,342 | 36 | atp9;rps10 | False | ON930432.1; 415,837 bp; 54 genes |
| drParJuda1 | oatk.reads | pltd | 2021-12-14 | 152,629 | 107 | atpF;rps16 | True | NC_066035.1; 152,689 bp; 130 genes |
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