Strain Descriptions

F11

About the F11 strain of Mycobacterium tuberculosis

We have completed the sequencing of a representative isolate of the F11 strain, which is found in large clusters around the world, particularly in South Africa.

Dr. Tommie Victor of Stellenbosch University, South Africa, provided the F11 genomic DNA for sequencing.

Our specific aims for the F11 sequencing project as follows:

  1. Generate and assemble sequence reads yielding 8X coverage of the M. tuberculosis F11 genome through whole genome shotgun sequencing.
  2. Perform automated annotation of the sequence assembly.
  3. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.

Data Releases

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting 22.27X assembly was made public in October, 2005, and the results of automated genome annotation will be made public in future releases.

Assembly Data for F11 strain, Assembly 1, 8/19/2005

  • 22.27X sequencing coverage of the genome
  • All 40 contigs are mapped to a single supercontig (scaffold) of 4.4 Mb
  • 110.1 Kb average contig length (range 2.4 - 570.3 Kb)
  • 4.4 Mb total length of combined contigs (4,405,268 bp)
  • Average base lies in a contig of length 182.2 Kb

C

About the C strain of Mycobacterium tuberculosis

The C strain has been highly transmitted in New York City. In one study this strain was found to be more common among injection drug users and resistant to reactive nitrogen intermediates. (Friedman et al. J Infect Dis. 1997 Aug;176(2):478-84.)

Dr. Barry Kreiswirth of the Public Health Research Institute, Newark, NJ, provided the genomic DNA for the C strain sequencing.

Our specific aims for the C sequencing project are as follows:

  1. Generate and assemble sequence reads yielding 5X coverage of the M. tuberculosis C genome through whole genome shotgun sequencing.
  2. Perform automated annotation of the sequence assembly.
  3. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.

Data Releases

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts). The resulting 6.7x(5.7x Q>20) assembly was made public in November, 2005, and the results of automated genome annotation will be made public in future releases.

Assembly Data for C strain, Assembly 1, 9/30/2005

  • 6.7x(5.7x Q>20) sequencing coverage of the genome
  • 160 contigs in 4 supercontigs (scaffolds)
  • 26.7 Kb average contig length (range 2.0 - 153.0 Kb)
  • 1.1 Mb average supercontig length (range 98.3 Kb - 3.0 Mb)
  • 4.3 Mb total length of combined contigs (4,276,200 bp)
  • Average base lies in a contig of length 47.4 Kb
  • Average base lies within a supercontig of length 3.0 Mb

Haarlem

About the Haarlem strain of Mycobacterium tuberculosis

Members of the Haarlem family of M. tuberculosis strains have been found in many parts of the world. The first representative of the family was discovered in Haarlem, The Netherlands.

The strain was provided by Barry Kreisworth, Public Health Research Institute.

Data Releases

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts). The resulting 14.57x (11.15x Q>20) assembly was made public in September, 2006, and the results of automated genome annotation will be made public in future releases.

Assembly Data for Haarlem strain, Assembly 1, 7/12/2006

  • 14.57x(11.15x Q>20) sequencing coverage of the genome
  • 65 contigs in 8 supercontigs (scaffolds)
  • 4.3 Mb total length of combined contigs (4,347,292 bp)
  • Average base lies in a contig of length 111.6 Kb
  • Average base lies within a supercontig of length 2.5 Mb