Taxonomy

Metdbid	METDB_00278
Kingdom	Eukaryota
Supergroup	Stramenopiles
Phylum	Ochrophyta
Class	Chrysophyseae
Order	Chryso_Clade_C
Family	Chromulinaceae
Genus	Ochromonas
Species	triangulata
Strain name	RCC21
Strain name synonyms	CHR25
TaxNCBI	1955567
TaxWoRMS
Readset (paired)	RCC21 - ERR3497269
Annotation search	Link to associated annotation search function

Environmental parameters

Longitude	-4.13
Latitude	47.9
Site	Atlantic Ocean
Site description	Bay of Biscay
Country	FRANCE
Habitat	marine habitat

Assembly metrics

Percentage of remapping of all readsets on transcriptom	95.9%
Percentage of good mapping	90%
Number of contigs	44,109
Largest contig	23,703
Number of bases	59,359,190
Contigs average lenght	1345.7
Number of contigs with orf	25,651
n50	1,922
GC	0.39793
Transcriptome analysis project
Origin of the datasets	RCC
Assembly Type	paired
Trinity version	trinity-v2.4.0

Annotation metrics

Transdecoder: Number of predicted proteins	29407
BUSCO against eukaryota_odb9	Complete BUSCOs 87.13% (264) Complete and single-copy BUSCOs 53.47% (162) Complete and duplicated BUSCOs 33.66% (102) Fragmented BUSCOs 4.29% (13) Missing BUSCOs 8.58% (26) Total BUSCO groups searched 100.00% (303)
Interproscan: Number of proteins with interproscan match	Pfam 26112 Interproscan ID 71976 Gene ontology ID 38261.0 KEGG ID 3311.0 PRINTS 11519
Cmsearch	tRNA 6 tmRNA 0 SSU_rRNA_eukarya 0 LSU_rRNA_eukarya 0 5_8S_rRNA 0 Others 0
Diamond against Uniref90_v7-2019	111545

Associated result files

Reference Assembly

Contigs fasta file	RCC-METDB_00278-ochromonas-triangulata-chr25-paired.fasta

Reads remapping to assembly

Quantification file (sf)	quant.sf
Metadata info (json)	RCC_ochromonas-triangulata-chr25_salmon-v0.9.1_roscoff.json

Assembly metrics

Assembly metrics file (csv)	RCC_ochromonas-distigma-chr25_transrate-v1.0.2_roscoff.csv
Contigs metrics (csv)	contigs.csv
Contigs with bad mapping (fasta)	bad.trinity_Ochromonas_distigma_RCC21_BAS.fasta.gz
Contigs with good mapping (fasta)	good.trinity_Ochromonas_distigma_RCC21_BAS.fasta.gz

Annotation files

Transdecoder: Find Coding Regions Within Transcripts	RCC-METDB_00278-ochromonas-triangulata-chr25-paired_cut.cleaned.fasta.transdecoder.pep
InterProscan: Protein sequence analysis and classification	RCC-METDB_00278-ochromonas-triangulata-chr25-paired_full_i5_annotations
Diamond: for aligning Transcripts against NCBI NR	RCC-METDB_00278-ochromonas-triangulata-chr25-paired.diamond_matches
Cmsearch: Use of Covariance model (CM) to search for homologous RNAs Within Transcriptoms	RCC-METDB_00278-ochromonas-triangulata-chr25-paired_cat_cmsearch_matches.tbl.deoverlapped
BUSCO: assessment of transcriptome completeness	RCC-METDB_00278-ochromonas-triangulata-chr25-paired_BUSCO_short_summary.txt

Quality file

Read quality file	BBD_BASOSW_3_1_C3YEPACXX.IND6_noribo_clean.fastq.gz.P.qtrim_fastqc.zip
Read quality file	BBD_BASOSW_3_2_C3YEPACXX.IND6_noribo_clean.fastq.gz.P.qtrim_fastqc.zip