NCBI taxon id: | 319673 NCBI; ENA; GoaT |
---|---|
Order: | Akentrogonida |
Family: | Clistosaccidae |
NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Crustacea;Multicrustacea;Cirripedia;Rhizocephala;Clistosaccidae;Clistosaccus; |
GoaT genome size (M): | 1,841 (ancestor) |
GoaT asm span (M): | 264 (ancestor) |
GoaT chr no.: | 34 (ancestor) |
GoaT haploid no.: | 8 (ancestor) |
GoaT ploidy: | 6 (ancestor) |
ToLID prefix: | qxCliPagu |
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 |
---|---|---|---|---|---|---|
qxCliPagu1 | SAN0000181 | SANGER INSTITUTE | FEMALE | GONAD | SAMEA7523196 | SAMEA7523100 |
qxCliPagu10 | SAN20000837 | SANGER INSTITUTE | FEMALE | WHOLE_ORGANISM | SAMEA12813522 | SAMEA12813473 |
qxCliPagu11 | SAN20000842 | SANGER INSTITUTE | FEMALE | WHOLE_ORGANISM | SAMEA12813528 | SAMEA12813478 |
qxCliPagu2 | SAN0000182 | SANGER INSTITUTE | FEMALE | GONAD | SAMEA7523197 | SAMEA7523101 |
qxCliPagu3 | SAN20000857 | SANGER INSTITUTE | FEMALE | WHOLE_ORGANISM | SAMEA12813426 | SAMEA12813425 |
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 | qxCliPagu1 | 31 | 36.34 | 5,048,421 | 80.87 | 3.55 | 87.49 | 3.25 | ![]() ![]() histogram.txt |
10x | qxCliPagu1 | 31 | 22.99 | 727,619,425 | 85.16 | 7.38 | 82.96 | 1.14 | ![]() ![]() histogram.txt |
hic-arima2 | qxCliPagu2 | 31 | 46.79 | 723,602,410 | 63.35 | 1.71 | 96.16 | 0.62 | ![]() ![]() histogram.txt |
pacbio | qxCliPagu9 | 31 | 110 | 950,645,254 | 63.56 | 1.19 | 91.66 | 0.30 | ![]() ![]() histogram.txt |
hic-arima2 | qxCliPagu9 | 31 | 44.36 | 1,373,254,499 | 0.00 | 100.00 | 2.92 | 0.25 | ![]() ![]() 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 | qxCliPagu1 | 2020-10-29 | 78010 | m64089_201029_104118 | A01 | 1020 | 1,024,838,178 | 11,222 | SAMEA7523196 | ||
PacBio - HiFi | qxCliPagu9 | 2023-05-08 | TRACTION-RUN-574 | m64228e_230508_055021 | F01 | 2054 | 22,872,403,196 | 15,960 | SAMEA12813521 | ||
PacBio - HiFi | qxCliPagu9 | 2024-02-23 | TRACTION-RUN-1140 | m84093_240223_154438_s4 | D01 | 2054 | 18,538,781,061 | 14,218 | SAMEA12813521 | ||
PacBio - HiFi (ULI) | qxCliPagu9 | 2024-04-30 | TRACTION-RUN-1259 | m84098_240430_105248_s3 | B01 | 2005 | 58,978,616,878 | 8,385 | SAMEA12813521 | ||
PacBio - HiFi | qxCliPagu9 | 2024-05-31 | TRACTION-RUN-1312 | m84047_240531_133150_s1 | A01 | 2073 | 68,296,461,977 | 15,522 | SAMEA12813521 | ||
PacBio - HiFi | qxCliPagu9 | 2024-06-18 | TRACTION-RUN-1333 | m84098_240618_114443_s4 | D01 | 2054 | 61,156,254,505 | 11,742 | SAMEA12813521 |
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 |
---|---|---|---|---|---|---|---|---|---|
Chromium genome | qxCliPagu1 | 2020-10-27 | 35278_8#5 | 124,683,580 | 18,827,220,580 | SAMEA7523196 | qc complete | ||
Chromium genome | qxCliPagu1 | 2020-10-27 | 35278_8#7 | 101,487,538 | 15,324,618,238 | SAMEA7523196 | qc complete | ||
Chromium genome | qxCliPagu1 | 2020-10-27 | 35278_8#8 | 100,158,776 | 15,123,975,176 | SAMEA7523196 | qc complete | ||
Chromium genome | qxCliPagu1 | 2020-10-27 | 35278_8#6 | 109,847,212 | 16,586,929,012 | SAMEA7523196 | qc complete | ||
Hi-C - Arima v2 | qxCliPagu2 | 2020-11-14 | 35430_3#4 | 677,655,470 | 102,325,975,970 | SAMEA7523197 | qc complete | ||
Hi-C - Arima v2 | qxCliPagu9 | 2024-01-26 | 48341_6-7#1 | 1,100,267,908 | 166,140,454,108 | SAMEA12813521 | qc complete | ||
RNA PolyA | qxCliPagu6 | 2023-11-02 | 48017_1#85 | 57,197,170 | 8,636,772,670 | SAMEA12813518 | qc complete |
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 |
---|---|
0.97809 | [2 seqs] NZ_FSRF01000002.1 Pseudoalteromonas sp. 13-15, whole genome shotgun sequence [...] |
0.960395 | [2 seqs] NZ_LGBR01000001.1 Polaribacter dokdonensis DSW-5 contig1, whole genome shotgun sequence [...] |
0.93735 | [2 seqs] NZ_CP012160.1 Octadecabacter temperatus strain SB1, complete genome [...] |
0.934853 | [21 seqs] NZ_AULQ01000001.1 Mesoflavibacter zeaxanthinifaciens DSM 18436 H574DRAFT_scaffold00001.1_C, whole genome shotgun sequence [...] |
0.934669 | [114 seqs] NZ_MKKN01000001.1 Vibrio sp. 10N.222.47.A9 10N.222.47.A9_contig_1, whole genome shotgun sequence [...] |
0.934669 | [2 seqs] NC_011059.1 Prosthecochloris aestuarii DSM 271, complete genome [...] |
0.933552 | [2 seqs] NZ_LGBR01000001.1 Polaribacter dokdonensis DSW-5 contig1, whole genome shotgun sequence [...] |
0.932601 | [21 seqs] NZ_LOFG01000001.1 Pseudoalteromonas sp. H103 scaffold_1, whole genome shotgun sequence [...] |
0.927097 | [2 seqs] NZ_CP012160.1 Octadecabacter temperatus strain SB1, complete genome [...] |
0.925107 | [139 seqs] NZ_LNDJ01000001.1 Psychrobacter piscatorii strain LQ58 contig1, whole genome shotgun sequence [...] |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
---|---|---|---|
qxCliPagu9 | ptg000598c | 1522 |
|
qxCliPagu9 | ptg000632l | 660 |
|
qxCliPagu9 | ptg000636l | 660 |
|
qxCliPagu9 | ptg001014l | 1519 |
|
qxCliPagu9 | ptg001177l | 1518 |
|
qxCliPagu9 | ptg001262l | 1767 |
|
qxCliPagu9 | ptg001391l | 1521 |
|
qxCliPagu9 | ptg001642l | 1518 |
|
qxCliPagu9 | ptg002084l | 1523 |
|
qxCliPagu9 | ptg002126l | 1460 |
|
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 |
---|---|---|---|---|---|---|---|---|---|
qxCliPagu9 | hifiasm.purging | 2024-07-06 | 1,921,471 | 8,847 | 1,589,249,356 | C:91.8%[S:80.8%,D:11.0%],F:3.7%,M:4.5%,n:1013 | Q50.9-C89.5(HiFi) | ||
qxCliPagu9 | hifiasm.scaffolding.yahs | 2024-07-06 | 1,530,000 | 9,389 | 45,008,755 | 7,784 | 1,589,570,356 | C:92.1%[S:83.3%,D:8.8%],F:3.3%,M:4.6%,n:1013 | Q50.9-C89.5(HiFi) |
qxCliPagu9 | hifiasm | 2024-07-06 | 1,345,108 | 16,943 | 4,252,308,217 | C:92.9%[S:2.8%,D:90.1%],F:3.1%,M:4.0%,n:1013 | Q52.7-C99.1(HiFi) | ||
qxCliPagu9 | hifiasm-hic.purging | 2024-07-06 | 1,077,989 | 9,600 | 1,530,028,728 | C:91.3%[S:81.3%,D:10.0%],F:4.0%,M:4.7%,n:1013 | Q51.0-C87.5(HiFi) | ||
qxCliPagu9 | hifiasm-hic.hap1 | 2024-07-06 | 687,108 | 23,230 | 4,701,069,819 | C:93.0%[S:3.1%,D:89.9%],F:2.9%,M:4.1%,n:1013 | Q52.9-C99.1(HiFi) | ||
qxCliPagu9 | hifiasm-hic.scaffolding_hap2.yahs | 2024-07-06 | 515,417 | 13,621 | 3,218,415,383 | C:92.3%[S:5.3%,D:87.0%],F:3.4%,M:4.3%,n:1013 | Q54.4-C99.1(HiFi) | ||
qxCliPagu9 | hifiasm-hic.hap2 | 2024-07-06 | 674,702 | 9,957 | 3,218,415,383 | C:92.4%[S:5.0%,D:87.4%],F:3.4%,M:4.2%,n:1013 | Q54.4-C99.1(HiFi) | ||
qxCliPagu9 | hifiasm-hic.purging | 2024-02-27 | 994,802 | 3,105 | 1,024,817,115 | C:90.8%[S:83.1%,D:7.7%],F:3.9%,M:5.3%,n:1013 | Q53.4-C88.1(HiFi) | ||
qxCliPagu9 | hifiasm-hic.hap1 | 2024-02-27 | 400,719 | 19,134 | 2,672,009,808 | C:92.2%[S:12.3%,D:79.9%],F:3.4%,M:4.4%,n:1013 | Q51.4-C98.5(HiFi) | ||
qxCliPagu9 | hifiasm-hic.scaffolding_hap2.yahs | 2024-02-27 | 519,210 | 10,758 | 640,204 | 10,373 | 2,122,264,950 | C:91.2%[S:16.3%,D:74.9%],F:3.6%,M:5.2%,n:1013 | Q52.8-C98.5(HiFi) |
qxCliPagu9 | hifiasm-hic.hap2 | 2024-02-27 | 603,242 | 8,838 | 2,122,187,950 | C:91.2%[S:14.7%,D:76.5%],F:3.7%,M:5.1%,n:1013 | - | ||
qxCliPagu9 | hifiasm.purging | 2024-02-27 | 1,675,320 | 2,055 | 1,029,249,894 | C:91.4%[S:84.0%,D:7.4%],F:3.7%,M:4.9%,n:1013 | Q53.7-C95.9(HiFi) | ||
qxCliPagu9 | hifiasm.scaffolding.yahs | 2024-02-27 | 1,626,296 | 2,279 | 53,791,870 | 1,285 | 1,029,448,694 | C:91.6%[S:84.8%,D:6.8%],F:3.5%,M:4.9%,n:1013 | Q53.7-C95.9(HiFi) |
qxCliPagu9 | hifiasm | 2024-02-27 | 692,317 | 14,748 | 2,788,803,723 | C:92.3%[S:6.2%,D:86.1%],F:3.3%,M:4.4%,n:1013 | Q51.4-C98.6(HiFi) |
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
---|---|---|---|---|---|---|---|---|---|
qxCliPagu9 | mitohifi.hifiasm-hic | mito | 2024-02-27 | 62,873 | 30 | None | True | 1 | MZ411548.1; 14,579 bp; 37 genes |
qxCliPagu9 | mitohifi.hifiasm | mito | 2024-02-27 | 38,229 | 30 | None | True | 1 | MZ411548.1; 14,579 bp; 37 genes |