Methanobrevibacter smithii

Data

NCBI

1 complete + 2 draft assembly strains:

Methanobrevibacter smithii ATCC 35061

• complete: NC_009515.1
• 1,853,160bp
• Ref: /fs/szdata/ncbi/ftp.ncbi.nih.gov/genomes/Bacteria/Methanobrevibacter_smithii_ATCC_35061/*fna
• Published: Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut PNAS
• Assembled: Phrap and PCAP

Methanobrevibacter smithii DSM 2374

• draft: NZ_ABYV02000000
• 1,727,775 bp
• 25 contigs: NZ_ABYV02000001 .. NZ_ABYV02000025

Methanobrevibacter smithii DSM 2375

• draft: NZ_ABYW00000000
• 1,704,865 bp
• 24 contigs: NZ_ABYW01000001 .. NZ_ABYW01000024

Methanobrevibacter smithii DSM 11975

• progress

WUSTL (Gordon Lab)

• Ftp:

 http://cgsweb.wustl.edu/~hansene/

• Location:

 /fs/szattic-asmg4/methanobrevibacter_smithii/Data

• 22 strains
• half-way through sequencing (should have all the data by early to mid-January)
• right now (--Dpuiu 15:19, 15 December 2009 (EST)):
  • 10 strains sequenced by GAII Illumina (36mers) with 3-8 million reads per strain (coverage is 50-150x),
  • 12 strains sequenced by 454-Titanium sequencing, with 20,000 to 90,000 reads per strain (coverage is ~5-20x).

Illumina: 36 bp single reads

   nl  strain      reads   bases       cvg
    1  FR1LH1      5186537 186715332   100
    2  FR1LH3      7211080 259598880   140
    3  FR1LH6      4968262 178857432   96
    4  TS145A      6536457 235312452   126
    5  TS145B      8277390 297986040   160
    6  TS94-3      4886376 175909536   94
    7  TS94-5      4785200 172267200   92
    8  TS95-2      2896065 104258340   56
    9  TS95-3      5064150 182309400   98
   10  TS95-4      3557512 128070432   69
   11  TS95-5      4559830 164153880   88

454: avg 342 bp single reads

   nl  strain      reads   bases       cvg
    1  TS145A      83667   28587141    15
    2  TS145B      45203   15720997    8
    3  TS146-3     49854   17608862    10
    4  TS146e4     58633   18306825    10
    5  TS146e5A    27844   8311560     4
    6  TS146e5B    73182   23547825    13
    7  TS147e8     68487   20662109    11
    8  TS94-3      449545  157306990   85
    9  TS94-5      76513   26734802    14
   10  TS95-2      73255   25779806    14
   11  TS95-4      85737   29231201    16
   12  TS95-5      96757   35000794    19

Illumina & 454 : 7 strands have both Illumina & 454 reads

   nl  strand          #reads  #bases          cvg     #read   #bases          cvg
    1  FR1LH1          5186537 186715332       100     .       .               .
    2  FR1LH3          7211080 259598880       140     .       .               .       
    3  FR1LH6          4968262 178857432       96      .       .               .       
    4* TS145A          6536457 235312452       126     83667   28587141        15
    5* TS145B          8277390 297986040       160     45203   15720997        8       
    6  TS146-3         .       .               .       49854   17608862        10
    7  TS146e4         .       .               .       58633   18306825        10
    8  TS146e5A        .       .               .       27844   8311560         4
    9  TS146e5B        .       .               .       73182   23547825        13
   10  TS147e8         .       .               .       68487   20662109        11
   11* TS94-3          4886376 175909536       94      449545  157306990       85      
   12* TS94-5          4785200 172267200       92      76513   26734802        14
   13* TS95-2          2896065 104258340       56      73255   25779806        14
   14  TS95-3          5064150 182309400       98      .       .               .       
   15* TS95-4          3557512 128070432       69      85737   29231201        16
   16* TS95-5          4559830 164153880       88      96757   35000794        19