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. 2018 Oct 25;7(16):e01293-18. doi: 10.1128/MRA.01293-18

TABLE 1.

Sequencing metrics and genomic data for A. molluscorum strain LMG 25693T

Feature Value(s)a
Sequencing metrics
    454 (shotgun) platform
        No. of reads 177,873
        No. of bases 73,714,660
        Average length (bases) 414.4
        Coverage (×) 26.3
    454 (paired-end) platform
        No. of reads 150,593
        No. of bases 46,384,064
        Average length (bases) 308.0
        Coverage (×) 16.6
    Illumina HiSeq 2000 platform
        No. of reads 25,306,576
        No. of bases 2,530,657,600
        Average length (bases) 100
        Coverage (×) 903.6
    PacBio platform
        No. of reads 129,047
        No. of bases 399,548,656
        Average length (bases) 3,096.1b
        Coverage (×) 142.7
    Newbler metricsc
        N50ContigSize (454) (bases) 90,324
        Q40PlusBases (454) (%) 99.84
        N50ContigSize (HiSeq pool 1) (bases) 78,972
        Q40PlusBases (HiSeq pool 1) (%) 99.99
        N50ContigSize (HiSeq pool 2) (bases) 90,503
        Q40PlusBases (HiSeq pool 2) (%) 99.96
        N50ContigSize (HiSeq pool 3) (bases) 79,027
        Q40PlusBases (HiSeq pool 3) (%) 99.97
Genomic data
    Chromosome
        Size (bp) 2,800,582
        G+C content (%) 26.25
        No. of CDSd 2,666
            Assigned function (% CDS) 1,044 (39.2)
            General function annotation (% CDS) 995 (37.3)
            Domain/family annotation only (% CDS) 199 (7.5)
            Hypothetical (% CDS) 428 (16.1)
        Pseudogenes 31
    Genomic islands/CRISPR
        No. of genetic islands 3
        No. of CDS in genetic islands 71, [1]
        CRISPR-Cas loci I-B, [III-A]
    Gene content/pathways
        IS elements, mobile elements, or tranposases 3 (IS1595); 1, [1] (other)
        Signal transduction
            Che proteins cheABDRVW(Y)2
            No. of methyl-accepting chemotaxis proteins 26
            No. of response regulators 57
            No. of histidine kinases 62
            No. of response regulator/histidine kinase fusions 7
            No. of diguanylate cyclases 17
            No. of diguanylate phosphodiesterases (HD-GYP, EAL) 4, 5
            No. of diguanylate cyclase/phosphodiesterases 8
            No. of other 11
        Motility
            Flagellin genes fla1 to fla6
        Restriction/modification
            No. of type I systems (hsd) 1
            No. of type II systems 1, [1]
            No. of type III systems 0
        Transcription/translation
            No. of transcriptional regulatory proteins 64
            Non-ECFe σ factors σ54, σ70
            No. of ECF σ factors 0
            No. of tRNAs 56
            No. of ribosomal locif 3 (A), 3 (B)
        CO dehydrogenase (coxSLF) Yes
        Ethanolamine utilization (eutBCH) Yes
        Nitrogen fixation (nif) Yes
        Osmoprotection BCCT3, ectABC
        Pyruvate → acetyl-CoA
            Pyruvate dehydrogenase (E1/E2/E3) Yes
            Pyruvate:ferredoxin oxidoreductase por
        Urease ureAB
        Vitamin B12 biosynthesis Yes
a

Numbers in square brackets indicate pseudogenes or fragments.

b

Maximum length, 25,747 bases.

c

Features and values taken from largeContigMetrics within 454NewblerMetrics.txt for each assembly. Large contigs were defined as ≥500 bases. Due to the large number of HiSeq reads, the total reads were split into three pools and assembled independently.

d

Numbers do not include pseudogenes; CDS, coding sequences.

e

ECF, extracytoplasmic function.

f

A: 16S-tRNAIle-tRNAAla-23S-5S; B: 16S-23S-5S.

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