Light emerald
NCBI taxon id: | 934813 NCBI; ENA; GoaT |
---|---|
Order: | Lepidoptera |
Family: | Geometridae |
NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Geometroidea;Geometridae;Ennominae;Campaea; |
GoaT genome size (M): | 831 (ancestor) |
GoaT asm span (M): | 335 (direct) |
GoaT chr no.: | 62 (direct) |
GoaT haploid no.: | 31 (direct) |
GoaT ploidy: | 2 (ancestor) |
ToLID prefix: | ilCamMarg |
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 |
---|---|---|---|---|---|---|
ilCamMarg1 | Ox000674 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7701722 | SAMEA7701535 |
ilCamMarg1 | Ox000674 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7701721 | SAMEA7701535 |
ilCamMarg1 | Ox000674 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7701721 | SAMEA7701535 |
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 |
---|---|---|---|---|---|---|---|---|---|
10x | ilCamMarg1 | 31 | 57.8 | 364,296,457 | 26.18 | 0.56 | 96.07 | 0.38 | histogram.txt |
pacbio | ilCamMarg1 | 31 | 125.5 | 142,600,556 | 20.05 | 100.00 | 91.83 | 0.67 | histogram.txt |
hic-arima2 | ilCamMarg1 | 31 | 131.2 | 418,697,436 | 61.46 | 0.86 | 98.94 | 0.37 | 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 | ilCamMarg1 | 2021-05-02 | 81871 | m64221e_210502_042236 | C01 | 1003 | 17,078,868,189 | 15,022 | SAMEA7701722 | ERR6454734 | |
PacBio - HiFi | ilCamMarg1 | 2021-06-15 | 83254 | m64222e_210615_183345 | D01 | 1003 | 27,166,040,128 | 14,861 | SAMEA7701722 | ERR6939214 |
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 | ilCamMarg1 | 2021-04-06 | 37204_4#19 | 105,977,078 | 16,002,538,778 | SAMEA7701722 | ERR6054361 | qc complete | Campaea margaritaria (1.00) |
Chromium genome | ilCamMarg1 | 2021-04-06 | 37204_4#18 | 124,454,174 | 18,792,580,274 | SAMEA7701722 | ERR6054360 | qc complete | Campaea margaritaria (1.00) |
Chromium genome | ilCamMarg1 | 2021-04-06 | 37204_4#17 | 112,736,330 | 17,023,185,830 | SAMEA7701722 | ERR6054359 | qc complete | Campaea margaritaria (1.00) |
Chromium genome | ilCamMarg1 | 2021-04-06 | 37204_4#20 | 87,209,786 | 13,168,677,686 | SAMEA7701722 | ERR6054362 | qc complete | Campaea margaritaria (1.00) |
Hi-C - Arima v2 | ilCamMarg1 | 2021-03-22 | 36943_1#4 | 1,013,406,358 | 153,024,360,058 | SAMEA7701721 | ERR6054358 | qc complete | Campaea margaritaria (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 |
---|---|
0.999713 | [120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...] |
0.983159 | [23 seqs] NZ_JRXV01000021.1 Pseudomonas fluorescens strain AU10973 Contig_17, whole genome shotgun sequence [...] |
0.978165 | [2 seqs] NZ_CP015639.1 Pseudomonas fluorescens strain L228, complete genome [...] |
0.964587 | [122 seqs] NZ_CVTU01000121.1 Pseudomonas sp. 44 R 15, whole genome shotgun sequence [...] |
0.964587 | [42 seqs] NZ_MIKC01000001.1 Enterococcus ureilyticus strain LMG 26676, whole genome shotgun sequence [...] |
0.919083 | [12 seqs] NZ_LCTG01000001.1 Gluconobacter oxydans strain NL71 Scaffold1_1, whole genome shotgun sequence [...] |
0.916433 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
0.909049 | [32 seqs] NZ_KN050720.1 Rahnella sp. WP5 EX31DRAFT_scaffold00001.1, whole genome shotgun sequence [...] |
0.903605 | [92 seqs] NZ_JRXE01000001.1 Erwinia iniecta strain B120 contig000001, whole genome shotgun sequence [...] |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
---|---|---|---|
No matching records found |
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):
BTK datasets:
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
---|---|---|---|---|---|---|---|---|---|
ilCamMarg1 | hicanu.purging | 2021-05-11 | 8,952,748 | 194 | 342,894,748 | C:98.9%[S:98.5%,D:0.4%],F:0.5%,M:0.6%,n:1367 | - | ||
ilCamMarg1 | hicanu | 2021-05-11 | 2,123,462 | 1,734 | 705,174,881 | C:99.0%[S:69.3%,D:29.7%],F:0.5%,M:0.5%,n:1367 | - | ||
ilCamMarg1 | hifiasm | 2021-05-11 | 11,935,394 | 145 | 347,154,596 | C:99.0%[S:98.6%,D:0.4%],F:0.4%,M:0.6%,n:1367 | - | ||
ilCamMarg1 | hifiasm.purging | 2021-05-11 | 11,935,394 | 120 | 344,560,397 | C:99.0%[S:98.7%,D:0.3%],F:0.4%,M:0.6%,n:1367 | - | ||
ilCamMarg1 | hifiasm.scaff.salsa | 2021-05-11 | 11,935,323 | 121 | 12,093,622 | 119 | 344,525,249 | - |
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
---|---|---|---|---|---|---|---|---|
No matching records found |