brown garden snail
NCBI taxon id: | 6535 NCBI; ENA; GoaT |
---|---|
Order: | Stylommatophora |
Family: | Helicidae |
NCBI lineage: | Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Mollusca;Gastropoda;Heterobranchia;Euthyneura;Panpulmonata;Eupulmonata;Stylommatophora;Helicina;Helicoidea;Helicidae;Cornu;Cornu; |
GoaT genome size (M): | 3,501 (direct) |
GoaT asm span (M): | 3,329 (ancestor) |
GoaT chr no.: | 54 (direct) |
GoaT haploid no.: | 18 (direct) |
GoaT ploidy: | 2 (ancestor) |
ToLID prefix: | xgCorAspe |
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 |
---|---|---|---|---|---|---|
xgCorAspe1 | SAN0001334 | SANGER INSTITUTE | HERMAPHRODITE_MONOECIOUS | NOT_COLLECTED | SAMEA9312772 | SAMEA9312697 |
xgCorAspe1 | SAN0001334 | SANGER INSTITUTE | HERMAPHRODITE_MONOECIOUS | NOT_COLLECTED | SAMEA9312771 | SAMEA9312697 |
xgCorAspe10 | SAN0001343 | SANGER INSTITUTE | HERMAPHRODITE_MONOECIOUS | HEAD | SAMEA9312924 | SAMEA9312910 |
xgCorAspe10 | SAN0001343 | SANGER INSTITUTE | HERMAPHRODITE_MONOECIOUS | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA9312927 | SAMEA9312910 |
xgCorAspe10 | SAN0001343 | SANGER INSTITUTE | HERMAPHRODITE_MONOECIOUS | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA9312944 | SAMEA9312910 |
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 |
---|---|---|---|---|---|---|---|---|---|
hic-arima2 | xgCorAspe2 | 31 | 60.22 | 2,595,709,653 | 61.94 | 1.90 | 96.00 | 0.40 | ![]() ![]() histogram.txt |
10x | xgCorAspe16 | 31 | 18.64 | 3,957,484,482 | 70.87 | 1.44 | 97.91 | 0.77 | ![]() ![]() histogram.txt |
pacbio | xgCorAspe16 | 31 | 28.97 | 2,551,459,674 | 58.88 | 1.71 | 95.38 | 0.11 | ![]() ![]() histogram.txt |
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 | xgCorAspe16 | 2021-05-23 | 82543 | m64178e_210523_030855 | C01 | 1019 | 1,790,115,920 | 10,273 | SAMEA8534533 | ||
PacBio - HiFi (ULI) | xgCorAspe16 | 2022-09-19 | TRACTION-RUN-260 | m64229e_220919_002025 | C01 | 1017 | 13,747,618,359 | 8,052 | SAMEA8534537 | ||
PacBio - HiFi | xgCorAspe16 | 2023-03-21 | TRACTION-RUN-497 | m64089e_230321_154130 | H01 | 1012 | 1,045,339,432 | 11,726 | SAMEA8534536 | ||
PacBio - HiFi | xgCorAspe16 | 2023-10-31 | TRACTION-RUN-914 | m64222e_231031_191050 | B01 | 2096 | 21,113,710,751 | 14,232 | SAMEA8534536 | ||
PacBio - HiFi | xgCorAspe16 | 2024-02-07 | TRACTION-RUN-1114 | m84093_240207_151706_s2 | D01 | 2005 | 75,909,766,724 | 12,407 | SAMEA8534534 | ||
PacBio - HiFi | xgCorAspe16 | 2024-02-15 | TRACTION-RUN-1125 | m84093_240215_130837_s4 | D01 | 2096 | 39,816,430,542 | 13,514 | SAMEA8534536 |
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 |
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 | xgCorAspe2 | 2022-09-13 | 45804_4#1 | 2,922,538,930 | 441,303,378,430 | SAMEA9312776 | qc complete | Cornu aspersum (0.99) | |
Chromium genome | xgCorAspe16 | 2021-07-28 | 39212_4#8 | 109,523,444 | 16,538,040,044 | SAMEA8534537 | qc complete | Cornu aspersum (1.00) | |
Chromium genome | xgCorAspe16 | 2021-07-28 | 39212_4#3 | 237,516,250 | 35,864,953,750 | SAMEA8534537 | qc complete | Cornu aspersum (1.00) | |
Chromium genome | xgCorAspe16 | 2021-07-28 | 39212_4#6 | 231,525,748 | 34,960,387,948 | SAMEA8534537 | qc complete | Cornu aspersum (1.00) | |
Chromium genome | xgCorAspe16 | 2021-07-28 | 39212_4#7 | 341,114,978 | 51,508,361,678 | SAMEA8534537 | qc complete | ||
Chromium genome | xgCorAspe16 | 2021-07-28 | 39212_4#2 | 9,483,272 | 1,431,974,072 | SAMEA8534537 | qc complete | ||
Chromium genome | xgCorAspe16 | 2021-07-28 | 39212_4#5 | 213,003,800 | 32,163,573,800 | SAMEA8534537 | qc complete | Cornu aspersum (1.00) | |
Chromium genome | xgCorAspe16 | 2021-07-28 | 39212_4#4 | 337,930,736 | 51,027,541,136 | SAMEA8534537 | qc complete | ||
Chromium genome | xgCorAspe16 | 2021-07-28 | 39212_4#1 | 222,024,174 | 33,525,650,274 | SAMEA8534537 | qc complete | Cornu aspersum (1.00) | |
RNA PolyA | xgCorAspe11 | 2023-06-22 | 47503_1#43 | 73,877,334 | 11,155,477,434 | SAMEA9312975 | qc complete | Cornu aspersum (1.00) |
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 |
---|---|
0.904322 | 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 |
---|---|---|---|
xgCorAspe16 | atg000069l | 1217 |
|
xgCorAspe16 | atg000121l | 974 |
|
xgCorAspe16 | atg000131l | 833 |
|
xgCorAspe16 | atg000156l | 1051 |
|
xgCorAspe16 | atg000227l | 1071 |
|
xgCorAspe16 | atg000307l | 1043 |
|
xgCorAspe16 | atg000404l | 727 |
|
xgCorAspe16 | atg000418l | 1087 |
|
xgCorAspe16 | atg000499l | 783 |
|
xgCorAspe16 | atg000508l | 1216 |
|
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 |
Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.
Features (colours represent quantile bins):
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
---|---|---|---|---|---|---|---|---|---|
xgCorAspe16 | hifiasm | 2024-02-11 | 1,029,061 | 6,871 | 3,345,493,147 | C:88.2%[S:67.0%,D:21.2%],F:2.5%,M:9.3%,n:5295 | Q39.3-C91.7(10X); Q54.9-C98.3(HiFi) | ||
xgCorAspe16 | hifiasm.scaffolding_alt.yahs | 2024-02-11 | 170,107 | 44,391 | 2,705,794,022 | C:64.3%[S:55.2%,D:9.1%],F:3.9%,M:31.8%,n:5295 | Q37.6-C91.7(10X); Q54.5-C98.3(HiFi) | ||
xgCorAspe16 | hifiasm.purging | 2024-02-11 | 1,140,284 | 4,754 | 2,919,971,635 | C:87.7%[S:71.5%,D:16.2%],F:2.5%,M:9.8%,n:5295 | Q40.5-C91.3(10X); Q55.0-C97.8(HiFi) | ||
xgCorAspe16 | hifiasm.scaffolding.yahs | 2024-02-11 | 1,089,006 | 5,493 | 101,307,351 | 1,057 | 2,920,858,835 | C:89.3%[S:72.2%,D:17.1%],F:2.3%,M:8.4%,n:5295 | Q40.5-C91.3(10X); Q55.0-C97.8(HiFi) |
xgCorAspe16 | hifiasm | 2024-02-19 | 1,266,650 | 5,709 | 3,309,894,001 | C:88.6%[S:67.2%,D:21.4%],F:2.5%,M:8.9%,n:5295 | Q39.7-C91.7(10X); Q55.5-C98.6(HiFi) | ||
xgCorAspe16 | hifiasm.scaffolding_alt.yahs | 2024-02-19 | 232,338 | 25,546 | 725,593 | 21,919 | 2,315,098,582 | C:66.8%[S:58.4%,D:8.4%],F:3.4%,M:29.8%,n:5295 | Q40.6-C91.3(10X); Q55.4-C98.0(HiFi) |
xgCorAspe16 | hifiasm.purging | 2024-02-19 | 1,378,356 | 3,940 | 2,930,726,070 | C:88.4%[S:71.8%,D:16.6%],F:2.5%,M:9.1%,n:5295 | Q41.1-C91.3(10X); Q55.5-C98.0(HiFi) | ||
xgCorAspe16 | hifiasm.scaffolding.yahs | 2024-02-19 | 1,312,268 | 4,549 | 100,834,318 | 824 | 2,931,471,070 | C:89.5%[S:72.4%,D:17.1%],F:2.4%,M:8.1%,n:5295 | Q41.1-C91.3(10X); Q55.5-C98.0(HiFi) |
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
---|---|---|---|---|---|---|---|---|---|
xgCorAspe16 | mitohifi.hifiasm | mito | 2024-02-11 | 14,043 | 37 | ND4L | True | 1 | JQ417196.1; 14,050 bp; 37 genes |
xgCorAspe16 | mitohifi.reads | mito | 2024-02-11 | 14,043 | 37 | ND4L | True | 1 | JQ417196.1; 14,050 bp; 37 genes |
xgCorAspe16 | mitohifi.hifiasm | mito | 2024-02-19 | 14,043 | 37 | ND4L | True | 1 | JQ417196.1; 14,050 bp; 37 genes |
xgCorAspe16 | mitohifi.reads | mito | 2024-02-19 | 14,043 | 37 | ND4L | True | 1 | JQ417196.1; 14,050 bp; 37 genes |