Table 2

Genome sequencing and metabolic SNP detection

Sequencing Parameter

S288c

CEN.PK113-7D


MAQ Software Determination


No. of Reads

5,301,907

6,603,200

Total No. of SNPs

3,032

27,868

Total No. of Non-Ambiguous SNPs

1,013

24,663

Total No. of Filtered SNPsA,B

311

13,787


Metabolism Focused Detection


Total No. of Metabolic Genes ConsideredC

782

782

Total No. of Metabolic Bases (bp)

1.16M

1.16M

No. of Aligned Reads

477,565

623,400

Total Gap Size (bp)

0

0

Metabolic Genome Percent Reference Coverage (%)

99.7

99.4

Total No. of Metabolic SNPs detected

36

939

Total No. Nonsynonymous Metabolic SNPs Detected

3

219

Percent of SNPs Detected Nonsynonymous (%)

8.3

23.3

Total No. of Metabolic Genes Containing SNP

14

158

Total No. of Metabolic Genes with Nonsynonymous SNP

3

85


Notes: Base pairs (bp). (A) Filtered SNPs determined based on cut-off criteria within the Mapping and Assembling with Quality (MAQ) software environment. (B) Detected SNPs with estimated error < 0.003% (C) The total number of genes classified as metabolic was based on the Saccharomyces Genome Database, Strain S288c, version 12.0. The "S288c" designation in Table 2 refers to the resequencing of S. cerevisiae S288c using Illumnia/Solexa sequencing technology.

Otero et al. BMC Genomics 2010 11:723   doi:10.1186/1471-2164-11-723

Open Data