Genome sc|0000340


Database

NCBI Assembly

Accession

GCA_028278955.1

Genomics

Accession
NCBI Assembly:GCA_028278955.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 94.87%
  • Contamination: 0.85%
  • Quality: 90.62
Ribosomal and transfer RNA genes
  • 2 16S rRNAs (up to 80.0%)
  • 1 23S rRNA (up to 67.0%)
  • tRNAs for 19 amino acids
Sequencing depth
24.0 ×
Source
Other features
  • G+C Content: 66.68%
  • Coding Density: 92.33%
  • Codon Table: 11
  • N50: 15,477 bp
  • Contigs: 225
  • Largest Contig: 53,800 bp
  • Assembly Length: 2,477,953 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Completeness and contamination were assessed with CheckM v1.1.0 using a lineage-specific workflow.

The 16S rRNA gene sequence did not fully assemble using the automated assembler, but the two contigs in the MAG can be manually or with CAP4 overlapped with 56 bp. The individual sequences are: 
>2784506828 16S rRNA. Bacterial SSU [Unclassified Actinobacteria Act4 m_cahh6 : Ga0307048_1014] (+)strand
AAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCA
TGTTGCTTAATTCGAGGCAACGCGAAGAACCTTACCTGGGTTTGACATGT
ACGGAAAAGCCATAGAGATATGGTGTCCTTCGGGGCCGTACACAGGTGGT
GCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAA
CGAGCGCAACCCTCGTCCTATGTTGCCAGCACGTAAAGGTGGGGACTCGT
AGGAGACCGCCGGGGTCAACTCGGAGGAAGGTGGGGACGACGTCAAGTCA
TCATGCCCCTTATATCCAGGGCTGCAAACATGCTACAATGGCCGGCACAA
CGGGCAGCGACACCGCGAGGTGGAGCGAATCCCTTAAAACCGGTCTCAGT
TCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAGTCGCTAGTAAT
CCCGGATCAGCAACGCCGGGGTGAATACGTTCCCGGGCCTTGTACACACC
GCCCGTCACACCACGAAAGTCGGCAACACCCGAAGTCAGTGGCCTAACTC
TTATGAGGGGGAGCTGCCGAAGGTGGGGTTGGCGATTGGGGTGAAGTCGT
AACAAGGTAGCCGTACCGGAAGGTGCGGCTGGATCACCTCCTTTCT

>2784507987 16S rRNA. Bacterial SSU [Unclassified Actinobacteria Act4 m_cahh6 : Ga0307048_1119] (+)strand
TGTTAACGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCC
TAACACATGCAAGTCGAACGAGGTCGCCTTCGGGCAATGACCTAGTGGCG
AACGGGTGCGTAACACGTGAGGAACCTGCCCCGAAGACTGGGACAACCAC
GGGAAACTGTGGCTAATACCAGATGCCCTCTCCTGATCGCATGATCGGAA
GAGGAAATGCTCCGGCGCTTCGGGAGGGCCTCGCGGCCTATCAGCTTGTT
GGTGAGGTAACGGCTCACCAAGGTATCGACGGGTAGCTGGTCTGAGAGGA
CGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTGCGGGAGGCA
GCAGTGGGGAATCTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGC
GTGGGGGATGAAGGCTCTCGGGTTGTAAACCCCTTTCAGCAGGGACGAAA
TTGACGGTACCTGCAGAAGAAGCCCCGGCCAACTACGTGCCAGCAGCCGC
GGTGACACGTAGGGGGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGAGC
TCGTAGGCGGTTTAGTAAGTCAGATGTGAAAGGTTGGGGCTCAACCCTAA
GACTGCATCCGATACTGCTATGACTAGAGTCCGGTAGAGGAGTGTGGAAT
TCCTGGTGTAGCGGTGAAATGCGCAGATATCAGGAGGAACACCGACGGCG
AAGGCAGCACTCTGGGCCGGCACTGACGCTCAGGAGCGAAAGCGTGGGTA
GCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGTTGGGCACT
AGGTGTGGGGCCTTATCAACGGGTTCCGTGCCGTAGCTAACGCATTAAGT
GCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACG
GGGGCCCGCACAAGCGGCGGAGCATGTTGC
Together the form the following contig:

>16S rRNSA contig
TGTTAACGGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAACACATGC
AAGTCGAACGAGGTCGCCTTCGGGCAATGACCTAGTGGCGAACGGGTGCGTAACACGTGA
GGAACCTGCCCCGAAGACTGGGACAACCACGGGAAACTGTGGCTAATACCAGATGCCCTC
TCCTGATCGCATGATCGGAAGAGGAAATGCTCCGGCGCTTCGGGAGGGCCTCGCGGCCTA
TCAGCTTGTTGGTGAGGTAACGGCTCACCAAGGTATCGACGGGTAGCTGGTCTGAGAGGA
CGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTGCGGGAGGCAGCAGTGGGGA
ATCTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCGTGGGGGATGAAGGCTCTCG
GGTTGTAAACCCCTTTCAGCAGGGACGAAATTGACGGTACCTGCAGAAGAAGCCCCGGCC
AACTACGTGCCAGCAGCCGCGGTGACACGTAGGGGGCGAGCGTTGTCCGGAATTATTGGG
CGTAAAGAGCTCGTAGGCGGTTTAGTAAGTCAGATGTGAAAGGTTGGGGCTCAACCCTAA
GACTGCATCCGATACTGCTATGACTAGAGTCCGGTAGAGGAGTGTGGAATTCCTGGTGTA
GCGGTGAAATGCGCAGATATCAGGAGGAACACCGACGGCGAAGGCAGCACTCTGGGCCGG
CACTGACGCTCAGGAGCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCA
CGCCGTAAACGTTGGGCACTAGGTGTGGGGCCTTATCAACGGGTTCCGTGCCGTAGCTAA
CGCATTAAGTGCCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACG
GGGGCCCGCACAAGCGGCGGAGCATGTTGCTTAATTCGAGGCAACGCGAAGAACCTTACC
TGGGTTTGACATGTACGGAAAAGCCATAGAGATATGGTGTCCTTCGGGGCCGTACACAGG
TGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCG
CAACCCTCGTCCTATGTTGCCAGCACGTAAAGGTGGGGACTCGTAGGAGACCGCCGGGGT
CAACTCGGAGGAAGGTGGGGACGACGTCAAGTCATCATGCCCCTTATATCCAGGGCTGCA
AACATGCTACAATGGCCGGCACAACGGGCAGCGACACCGCGAGGTGGAGCGAATCCCTTA
AAACCGGTCTCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAGTCGCTAG
TAATCCCGGATCAGCAACGCCGGGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGT
CACACCACGAAAGTCGGCAACACCCGAAGTCAGTGGCCTAACTCTTATGAGGGGGAGCTG
CCGAAGGTGGGGTTGGCGATTGGGGTGAAGTCGTAACAAGGTAGCCGTACCGGAAGGTGC
GGCTGGATCACCTCCTTTCT

This contig is not in the Genbank file, but represent the full-length 16S rRNA gene sequence.
Automated checks
Complete

Sample Metadata

Date
Collection Date: 2014-06
Location
Lat Lon: 18.816 S 147.633 E
Toponym
Geo Loc Name: Australia: Davies Reef, Great Barrier Reef
Environment
Sample Type: metagenomic assembly
Isolation Source: sponge tissue, high temperature high CO2
Env Broad Scale: coral reef [ENVO:00000150]
Env Local Scale: coral reef [ENVO:00000150]
Env Medium: sponge
Other
Host: Phyllospongia foliascens
Package
Ncbi Submission Package: MIMAG.host-associated.6.0
Biosamplemodel: MIMAG.host-associated
Additional Accessions
SAMN13227197, SAMN13227198, SAMN13227203
All retrieved samples

Metadata retrieved 5 months ago


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