Taxonomy

Metdbid	METDB_00299
Kingdom	Eukaryota
Supergroup	Rhizaria
Phylum	Cercozoa
Class	Filosa-Chlorarachnea
Order	Chlorarachnida
Family	Chlorarachnida_X
Genus	Partenskyella
Species	glossopodia
Strain name	RCC365
Strain name synonyms	PROSOPE_99
TaxNCBI	552666
TaxWoRMS	590920
Readset (paired)	RCC365
Readset (paired)	RCC365
Annotation search	Link to associated annotation search function

Environmental parameters

Longitude	15.62
Latitude	37.4
Site	Mediterranean Sea
Site description	missing
Country	missing
Habitat	marine habitat

Assembly metrics

Percentage of remapping of all readsets on transcriptom	81.9%
Percentage of good mapping	61
Number of contigs	63,741
Largest contig	12,120
Number of bases	72,266,007
Contigs average lenght	1133.7
Number of contigs with orf	37,904
n50	1,565
GC	0.46007
Transcriptome analysis project
Origin of the datasets	RCC
Assembly Type	paired
Trinity version	trinity-v2.4.0

Annotation metrics

Transdecoder: Number of predicted proteins	44842
BUSCO against eukaryota_odb9	Complete BUSCOs 78.88% (239) Complete and single-copy BUSCOs 41.91% (127) Complete and duplicated BUSCOs 36.96% (112) Fragmented BUSCOs 12.21% (37) Missing BUSCOs 8.91% (27) Total BUSCO groups searched 100.00% (303)
Interproscan: Number of proteins with interproscan match	Pfam 32154 Interproscan ID 86691 Gene ontology ID 46849.0 KEGG ID 4776.0 PRINTS 12827
Cmsearch	tRNA 167 tmRNA 0 SSU_rRNA_eukarya 0 LSU_rRNA_eukarya 0 5_8S_rRNA 0 Others 0
Diamond against Uniref90_v7-2019	158125

Associated result files

Reference Assembly

Contigs fasta file	RCC-METDB_00299-partenskyella-glossopodia-prosope_99-paired.fasta

Reads remapping to assembly

Metadata info (json)	RCC_partenskyella-glossopodia-prosope_99_salmon-v0.9.1_roscoff.json
Quantification file (sf)	quant.sf

Assembly metrics

Contigs with bad mapping (fasta)	bad.METDB-00299_partenskyella-glossopodia-prosope_99.fasta.gz
Contigs metrics (csv)	contigs.csv
Contigs with good mapping (fasta)	good.METDB-00299_partenskyella-glossopodia-prosope_99.fasta.gz
Assembly metrics file (csv)	RCC_partenskyella-glossopodia-prosope_99_transrate-v1.0.2_roscoff.csv

Annotation files

Transdecoder: Find Coding Regions Within Transcripts	RCC-METDB_00299-partenskyella-glossopodia-prosope_99-paired_cut.cleaned.fasta.transdecoder.pep
BUSCO: assessment of transcriptome completeness	RCC-METDB_00299-partenskyella-glossopodia-prosope_99-paired_BUSCO_short_summary.txt
Diamond: for aligning Transcripts against NCBI NR	RCC-METDB_00299-partenskyella-glossopodia-prosope_99-paired.diamond_matches
InterProscan: Protein sequence analysis and classification	RCC-METDB_00299-partenskyella-glossopodia-prosope_99-paired_full_i5_annotations
Cmsearch: Use of Covariance model (CM) to search for homologous RNAs Within Transcriptoms	RCC-METDB_00299-partenskyella-glossopodia-prosope_99-paired_cat_cmsearch_matches.tbl.deoverlapped

Quality file

Read quality file	APE_AARTOSW_4_2_D179NACXX.IND8_noribo_clean.fastq.gz.P.qtrim_fastqc.zip
Read quality file	APE_ABATOSW_5_1_D179NACXX.IND1_noribo_clean.fastq.gz.P.qtrim_fastqc.zip
Read quality file	APE_AARTOSW_4_1_D179NACXX.IND8_noribo_clean.fastq.gz.P.qtrim_fastqc.zip
Read quality file	APE_ABATOSW_5_2_D179NACXX.IND1_noribo_clean.fastq.gz.P.qtrim_fastqc.zip