Assembly Summary


Taxonomy

Metdbid METDB_00330
Kingdom Eukaryota
Supergroup Hacrobia
Phylum Haptophyta
Class Prymnesiophyceae
Order Phaeocystales
Family Phaeocystaceae
Genus Phaeocystis
Species rex
Strain name RCC678
Strain name synonyms He001206-D2-B1
TaxNCBI 1631190
TaxWoRMS
Readset (paired) RCC678 - ERR3497205
Annotation search Link to associated annotation search function

Environmental parameters

Longitude 7.9
Latitude 54.18
Site Atlantic Ocean
Site description North Sea
Country GERMANY
Habitat marine habitat

Legend for assembly and annotation metrics
  • Good
  • Acceptable
  • Bad

Assembly metrics

Percentage of remapping of all readsets on transcriptom 94.4%
Percentage of good mapping 83%
Number of contigs 117,315
Largest contig 7,831
Number of bases 74,000,272
Contigs average lenght 630.8
Number of contigs with orf 50,168
n50 873
GC 0.60233
Transcriptome analysis project
Origin of the datasets RCC
Assembly Type paired
Trinity version trinity-v2.4.0

Annotation metrics

Transdecoder: Number of predicted proteins 68797
BUSCO against eukaryota_odb9
Complete BUSCOs 82.18% (249)
Complete and single-copy BUSCOs 41.25% (125)
Complete and duplicated BUSCOs 40.92% (124)
Fragmented BUSCOs 12.87% (39)
Missing BUSCOs 4.95% (15)
Total BUSCO groups searched 100.00% (303)
Interproscan: Number of proteins with interproscan match
Pfam 39124
Interproscan ID 104601
Gene ontology ID 60919.0
KEGG ID 5525.0
PRINTS 17940
Cmsearch
tRNA 41
tmRNA 0
SSU_rRNA_eukarya 0
LSU_rRNA_eukarya 0
5_8S_rRNA 0
Others 0
Diamond against Uniref90_v7-2019 209655


Associated result files


Reference Assembly

Contigs fasta file RCC-METDB_00330-phaeocystis-rex-he001206-d2-b1-paired.fasta

Reads remapping to assembly

Quantification file (sf) quant.sf
Metadata info (json) RCC_phaeocystis-rex-he001206-d2-b1_salmon-v0.9.1_roscoff.json

Assembly metrics

Contigs metrics (csv) contigs.csv
Contigs with good mapping (fasta) good.METDB-00330_phaeocystis-rex-he001206-d2-b1.fasta.gz
Contigs with bad mapping (fasta) bad.METDB-00330_phaeocystis-rex-he001206-d2-b1.fasta.gz
Assembly metrics file (csv) RCC_phaeocystis-rex-he001206-d2-b1_transrate-v1.0.2_roscoff.csv

Annotation files

Cmsearch: Use of Covariance model (CM) to search for homologous RNAs Within Transcriptoms RCC-METDB_00330-phaeocystis-rex-he001206-d2-b1-paired_cat_cmsearch_matches.tbl.deoverlapped
Transdecoder: Find Coding Regions Within Transcripts RCC-METDB_00330-phaeocystis-rex-he001206-d2-b1-paired_cut.cleaned.fasta.transdecoder.pep
BUSCO: assessment of transcriptome completeness RCC-METDB_00330-phaeocystis-rex-he001206-d2-b1-paired_BUSCO_short_summary.txt
InterProscan: Protein sequence analysis and classification RCC-METDB_00330-phaeocystis-rex-he001206-d2-b1-paired_full_i5_annotations
Diamond: for aligning Transcripts against NCBI NR RCC-METDB_00330-phaeocystis-rex-he001206-d2-b1-paired.diamond_matches

Quality file

Read quality file BBD_AAAAOSW_2_1_C1JHLACXX.IND4_noribo_clean.fastq.P.qtrim_fastqc.zip
Read quality file BBD_AAAAOSW_2_2_C1JHLACXX.IND4_noribo_clean.fastq.P.qtrim_fastqc.zip