NCBI taxon id: | 2813772 NCBI; ENA; GoaT |
---|---|
Order: | Suessiales |
Family: | Symbiodiniaceae |
NCBI lineage: | Eukaryota;Sar;Alveolata;Dinophyceae;Suessiales;Symbiodiniaceae;Gerakladium; |
GoaT genome size (M): | 115 (ancestor) |
GoaT asm span (M): | 937 (ancestor) |
GoaT chr no.: | 24 (ancestor) |
GoaT haploid no.: | 5 (ancestor) |
GoaT ploidy: | 2 (ancestor) |
ToLID prefix: | pyGerJepo |
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 |
---|---|---|---|---|---|---|
pyGerJepo1 | UDUK0000095 | UNIVERSITY OF DERBY | NOT_APPLICABLE | WHOLE_ORGANISM | SAMEA8579652 | SAMEA8579611 |
pyGerJepo4 | UDUK0000098 | UNIVERSITY OF DERBY | NOT_APPLICABLE | WHOLE_ORGANISM | SAMEA8579655 | SAMEA8579614 |
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 | pyGerJepo4 | 31 | 103 | 203,208,384 | 0.00 | 38.59 | 1.77 | 0.04 | histogram.txt |
pacbio | pyGerJepo1 | 31 | 27.76 | 1,448,447,639 | 56.39 | 0.25 | 95.78 | 0.10 | histogram.txt |
hic-arima2 | pyGerJepo1 | 31 | 23.5 | 1,724,658,702 | 0.00 | 100.00 | 6.73 | 0.18 | 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 (ULI) | pyGerJepo1 | 2022-04-08 | TRACTION-RUN-87 | m64229e_220408_002506 | B01 | - | 23,327,646,643 | 9,347 | SAMEA8579652 | ERR12666671 | |
PacBio - HiFi (ULI) | pyGerJepo1 | 2024-01-05 | TRACTION-RUN-1042 | m84093_240105_155132_s3 | A01 | - | 59,838,537,684 | 9,266 | SAMEA8579652 | pending | |
PacBio - HiFi (ULI) | pyGerJepo4 | 2024-02-27 | TRACTION-RUN-1146 | m84093_240227_112544_s1 | A01 | 2042 | 42,536,768,127 | 10,339 | SAMEA8579655 |
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 | pyGerJepo1 | 2021-09-13 | 40749_1#7 | 708,146,344 | 106,930,097,944 | SAMEA8579652 | ERR12654651 | 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 |
---|---|
0.992513 | NC_013222.1 Robiginitalea biformata HTCC2501, complete genome |
0.987996 | [124 seqs] NZ_ACNO01000124.1 Rhodococcus erythropolis SK121 contig00004, whole genome shotgun sequence [...] |
0.987263 | [62 seqs] NZ_FNYY01000061.1 Marinovum algicola strain FF3, whole genome shotgun sequence [...] |
0.984932 | [378 seqs] NZ_LWEI01000001.1 Alcanivorax sp. HI0003 HI0003_c1, whole genome shotgun sequence [...] |
0.984738 | [181 seqs] NZ_JXMT01000001.1 Labrenzia aggregata strain LZB033 contig1, whole genome shotgun sequence [...] |
0.98125 | [38 seqs] NZ_LXYO01000001.1 Marinobacter sp. EhC06 A7_Contig1, whole genome shotgun sequence [...] |
0.968895 | [21 seqs] NZ_LXRF01000001.1 Marinobacter adhaerens strain PBVC038 contig_0, whole genome shotgun sequence [...] |
0.956847 | [47 seqs] NZ_MAYB01000010.1 Nitratireductor aquibiodomus strain EBB 35.1 NODE_10_length_108672_cov_46.7571_ID_2876, whole genome shotgun sequence [...] |
0.948163 | [5 seqs] NZ_LNUS01000004.1 Staphylococcus epidermidis strain AU23 map unlocalized plasmid unnamed contig_5, whole genome shotgun sequence [...] |
0.942602 | [44 seqs] NZ_LMFB01000001.1 Rhizobium sp. Root483D2 contig_1, whole genome shotgun sequence [...] |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
---|---|---|---|
pyGerJepo4 | atg000789l | 1521 |
|
pyGerJepo1 | atg001550l | 1800 |
|
pyGerJepo4 | atg002274l | 1798 |
|
pyGerJepo1 | atg004312l | 924 |
|
pyGerJepo4 | ptg000002l | 1520 |
|
pyGerJepo4 | ptg000003l | 1532 |
|
pyGerJepo4 | ptg000004l | 1517 |
|
pyGerJepo4 | ptg000006c | 1521 |
|
pyGerJepo4 | ptg000007c | 1515 |
|
pyGerJepo4 | ptg000008c | 1492 |
|
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 | ||
pyGerJepo1 | Alcanivoracaceae | 6,715 | 0.25 | - | C:2.4%[S:2.4%,D:0.0%],F:0.8%,M:96.8%,n:124 | 1 | 0.02Mb | 20 | C:99.7%[S:10.8%,D:88.9%],F:0.0%,M:0.3%,n:619 | 62 | 12.98Mb | 5,010 |
pyGerJepo1 | Balneolaceae | 84,988 | 3.15 | Too many reads - NA | C:97.6%[S:11.3%,D:86.3%],F:1.6%,M:0.8%,n:124 | 101 | 7.25Mb | 62,639 | - | 0.00Mb | ||
pyGerJepo1 | Cyclobacteriaceae | 55,059 | 2.04 | Too many reads - NA | C:60.8%[S:30.9%,D:29.9%],F:0.9%,M:38.3%,n:768 | 169 | 3.30Mb | 5,411 | - | 0.00Mb | ||
pyGerJepo1 | Flavobacteriaceae | 65,478 | 2.43 | Too many reads - NA | C:90.5%[S:57.8%,D:32.7%],F:1.4%,M:8.1%,n:733 | 122 | 6.43Mb | 12,794 | - | 0.00Mb | ||
pyGerJepo1 | Halieaceae | 23,295 | 0.86 | C:99.9%[S:0.2%,D:99.7%],F:0.0%,M:0.1%,n:913 | C:99.2%[S:96.1%,D:3.1%],F:0.2%,M:0.6%,n:913 | 7 | 4.23Mb | 19,061 | C:100.0%[S:4.8%,D:95.2%],F:0.0%,M:0.0%,n:124 | 38 | 11.09Mb | 2,043 |
pyGerJepo1 | Hyphomonadaceae | 4,040 | 0.15 | C:98.7%[S:1.2%,D:97.5%],F:0.7%,M:0.6%,n:432 | C:0.7%[S:0.7%,D:0.0%],F:0.2%,M:99.1%,n:432 | 3 | 0.04Mb | 23 | C:98.1%[S:85.6%,D:12.5%],F:0.2%,M:1.7%,n:432 | 24 | 4.15Mb | 2,691 |
pyGerJepo1 | Marinobacteraceae | 26,884 | 1 | C:100.0%[S:0.0%,D:100.0%],F:0.0%,M:0.0%,n:124 | C:92.3%[S:69.8%,D:22.5%],F:1.4%,M:6.3%,n:782 | 20 | 5.04Mb | 11,352 | C:98.8%[S:6.6%,D:92.2%],F:0.1%,M:1.1%,n:782 | 179 | 24.42Mb | 10,414 |
pyGerJepo1 | Parvibaculaceae | 32,159 | 1.19 | C:100.0%[S:0.2%,D:99.8%],F:0.0%,M:0.0%,n:432 | C:100.0%[S:98.4%,D:1.6%],F:0.0%,M:0.0%,n:432 | 8 | 3.74Mb | 29,374 | C:66.9%[S:50.8%,D:16.1%],F:0.8%,M:32.3%,n:124 | 79 | 2.89Mb | 271 |
pyGerJepo1 | Piscirickettsiaceae | 4,173 | 0.15 | C:99.4%[S:1.4%,D:98.0%],F:0.0%,M:0.6%,n:491 | C:47.7%[S:47.7%,D:0.0%],F:1.8%,M:50.5%,n:491 | 45 | 1.17Mb | 988 | C:98.8%[S:31.6%,D:67.2%],F:0.0%,M:1.2%,n:491 | 56 | 5.52Mb | 1,578 |
pyGerJepo1 | Reichenbachiellaceae | 45,742 | 1.7 | Too many reads - NA | C:95.5%[S:53.6%,D:41.9%],F:0.0%,M:4.5%,n:768 | 79 | 6.01Mb | 29,835 | - | 0.00Mb |
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 |
---|---|---|---|---|---|---|---|---|---|
pyGerJepo1 | hifiasm | 2022-06-09 | 145,797 | 10,527 | 900,342,416 | C:54.4%[S:38.0%,D:16.4%],F:11.7%,M:33.9%,n:171 | Q51.4-C94.2(HiFi) | ||
pyGerJepo1 | hifiasm | 2024-03-08 | 942,887 | 4,493 | 1,219,720,069 | C:70.2%[S:50.9%,D:19.3%],F:12.9%,M:16.9%,n:171 | Q52.2-C99.6(HiFi) | ||
pyGerJepo1 | hifiasm.purging | 2024-03-08 | 744,205 | 2,850 | 943,240 | 2,253 | 1,047,988,838 | Q52.3-C99.6(HiFi) | |
pyGerJepo1 | hifiasm.purging | 2024-03-08 | 949,659 | 2,253 | 1,072,731,441 | Q52.3-C99.6(HiFi) | |||
pyGerJepo1 | hifiasm.purging | 2024-03-08 | 741,058 | 3,299 | 929,542 | 2,720 | 1,074,427,239 | Q52.2-C99.6(HiFi) | |
pyGerJepo1 | hifiasm.purging | 2024-03-08 | 744,205 | 2,899 | 942,765 | 2,307 | 1,052,276,685 | Q52.3-C99.6(HiFi) | |
pyGerJepo1 | hifiasm.purging | 2024-03-08 | 948,063 | 2,307 | 1,076,963,740 | Q52.3-C99.6(HiFi) | |||
pyGerJepo1 | hifiasm.purging | 2024-03-08 | 937,273 | 2,720 | 1,094,344,224 | Q52.2-C99.6(HiFi) | |||
pyGerJepo1 | hifiasm.scaffolding.yahs | 2024-03-08 | 731,329 | 2,940 | 920,542 | 2,348 | 1,052,276,685 | - | |
pyGerJepo1 | hicanu.purging | 2022-08-19 | 284,624 | 8,609 | 1,116,047,981 | C:67.8%[S:49.7%,D:18.1%],F:13.5%,M:18.7%,n:171 | Q56.6-C95.5(HiFi) | ||
pyGerJepo1 | hicanu | 2022-08-19 | 263,894 | 15,256 | 1,257,742,003 | C:67.8%[S:49.1%,D:18.7%],F:13.5%,M:18.7%,n:171 | Q56.9-C100.0(HiFi) | ||
pyGerJepo4 | hifiasm.purging | 2024-03-01 | 542,514 | 2,279 | 470,725,775 | C:63.8%[S:46.8%,D:17.0%],F:8.2%,M:28.0%,n:171 | Q56.5-C99.7(HiFi) | ||
pyGerJepo4 | hifiasm | 2024-03-01 | 368,134 | 4,405 | 535,987,441 | C:64.4%[S:47.4%,D:17.0%],F:8.2%,M:27.4%,n:171 | Q55.7-C99.7(HiFi) | ||
pyGerJepo4 | hifiasm.scaffolding.yahs | 2024-03-01 | 409,844 | 3,374 | 502,451 | 3,301 | 470,740,375 | C:61.9%[S:44.4%,D:17.5%],F:9.4%,M:28.7%,n:171 | Q56.5-C99.7(HiFi) |
pyGerJepo1 | hifiasm-hic.hap1 | 2024-01-09 | 744,559 | 5,742 | 1,236,330,698 | C:69.0%[S:49.7%,D:19.3%],F:14.0%,M:17.0%,n:171 | Q52.0-C99.6(HiFi) | ||
pyGerJepo1 | hifiasm-hic.purging | 2024-01-09 | 767,874 | 3,834 | 1,146,152,286 | C:69.0%[S:50.3%,D:18.7%],F:14.0%,M:17.0%,n:171 | Q52.2-C96.6(HiFi) | ||
pyGerJepo1 | hifiasm-hic.hap2 | 2024-01-09 | 819,339 | 2,755 | 1,143,534,059 | C:68.4%[S:49.7%,D:18.7%],F:13.5%,M:18.1%,n:171 | - | ||
pyGerJepo1 | hifiasm-hic.scaffolding.yahs | 2024-01-09 | 751,660 | 3,897 | 1,146,152,286 | C:69.0%[S:50.3%,D:18.7%],F:14.0%,M:17.0%,n:171 | Q52.2-C96.6(HiFi) | ||
pyGerJepo1 | hifiasm | 2022-08-19 | 461,908 | 5,151 | 1,029,541,669 | C:63.1%[S:45.0%,D:18.1%],F:12.9%,M:24.0%,n:171 | Q53.3-C99.1(HiFi) | ||
pyGerJepo1 | hifiasm.purging | 2022-08-19 | 455,783 | 4,451 | 979,024,739 | C:63.1%[S:45.0%,D:18.1%],F:12.9%,M:24.0%,n:171 | Q53.2-C95.3(HiFi) | ||
pyGerJepo1 | hifiasm.scaffolding.salsa | 2022-08-19 | 453,999 | 4,455 | 456,944 | 4,437 | 979,033,739 | C:63.1%[S:45.0%,D:18.1%],F:12.9%,M:24.0%,n:171 | Q53.2-C95.3(HiFi) |
pyGerJepo1 | hifiasm.scaffolding.yahs | 2022-08-19 | 447,528 | 4,495 | 979,024,739 | C:63.1%[S:45.0%,D:18.1%],F:12.9%,M:24.0%,n:171 | Q53.2-C95.3(HiFi) | ||
pyGerJepo1 | hicanu | 2022-06-09 | 74,396 | 22,895 | 1,107,005,521 | C:63.2%[S:46.8%,D:16.4%],F:11.7%,M:25.1%,n:171 | Q56.8-C100.0(HiFi) | ||
pyGerJepo1 | hifiasm.purging.20240115 | 2024-01-09 | 852,695 | 3,110 | 1,120,628,368 | Q52.3-C96.7(HiFi) | |||
pyGerJepo1 | hifiasm.scaffolding.20240115.yahs | 2024-01-09 | 833,358 | 3,154 | 1,120,628,368 | - | |||
pyGerJepo1 | hifiasm.scaffolding.20240115.yahs | 2024-01-09 | 797,250 | 2,280 | 1,000,599,496 | - | |||
pyGerJepo1 | hifiasm.scaffolding.20240115.yahs | 2024-01-09 | 34,713 | 493 | 14,185,139 | - | |||
pyGerJepo1 | hifiasm.scaffolding.20240115.yahs | 2024-01-09 | 833,358 | 3,154 | 1,120,628,368 | - | |||
pyGerJepo1 | hifiasm | 2024-01-09 | 851,371 | 5,332 | 1,263,059,888 | C:69.6%[S:50.3%,D:19.3%],F:13.5%,M:16.9%,n:171 | Q52.3-C99.6(HiFi) | ||
pyGerJepo1 | hifiasm.purging | 2024-01-09 | 855,527 | 3,603 | 1,185,640,929 | C:69.6%[S:50.9%,D:18.7%],F:13.5%,M:16.9%,n:171 | Q52.3-C97.5(HiFi) | ||
pyGerJepo1 | hifiasm.scaffolding.yahs | 2024-01-09 | 836,680 | 3,668 | 1,185,640,929 | C:69.6%[S:50.9%,D:18.7%],F:13.5%,M:16.9%,n:171 | Q52.3-C97.5(HiFi) |
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
---|---|---|---|---|---|---|---|---|---|
pyGerJepo1 | mitohifi.hifiasm-hic | mito | 2022-08-19 | 47,363 | 2 | None | False | 1 | NC_064340.1; 47,310 bp; 59 genes |
pyGerJepo1 | mitohifi.hicanu | mito | 2022-08-19 | 17,428 | 8 | None | False | 1 | NC_064340.1; 47,310 bp; 59 genes |
pyGerJepo1 | mitohifi.reads | pltd | 2022-08-19 | 33,093 | 6 | None | False | 1 | LC716140.1; 100,773 bp; 28 genes |
pyGerJepo1 | mitohifi.reads | mito | 2022-08-19 | 13,269 | 5 | None | False | 1 | NC_064340.1; 47,310 bp; 59 genes |
pyGerJepo4 | mitohifi.hifiasm | mito | 2024-03-01 | 23,529 | 15 | None | False | 1 | NC_058286.1; 25,726 bp; 29 genes |
pyGerJepo1 | mitohifi.hifiasm-hic | mito | 2024-01-09 | 54,978 | 5 | None | False | 1 | MT941069.1; 41,256 bp; 47 genes |
pyGerJepo1 | mitohifi.hifiasm | mito | 2022-08-19 | 47,363 | 2 | None | False | 1 | NC_064340.1; 47,310 bp; 59 genes |
pyGerJepo1 | mitohifi.reads | mito | 2022-06-09 | 21,268 | 3 | None | False | 1 | NC_058286.1; 25,726 bp; 29 genes |
pyGerJepo1 | mitohifi.hifiasm | mito | 2024-01-09 | 16,060 | 9 | None | False | 1 | MT941069.1; 41,256 bp; 47 genes |