Table 2 Consensus variants.

From: Challenges and opportunities for strain verification by whole-genome sequencing

Gene

Function/Notes

Variant

differs from ref

Impact

GDC11 (YER025W)

eIF2 subunit (translation)

G > A

1691

missense

PPX1 (YHR201C)

hydrolyzes inorganic phosphate

C > T

1693

missense

TOR2 (YKL203C)

cell cycle

T > G

1693

missense

DYN1 (YKR054C)

cell cycle

G > T

1691

missense

SLA2 (YNL243W)

cell cycle

C > T

1691

missense

CDC1 (YDR182W)

cell cycle

G > T

1693

missense

SCH9 (YHR205W)

protein kinase

C > T

1693

synonymous

Intergenic

Near Met17 deletion

T > A

1691

intergenic

  1. Eight variants identified by both GATK and Samtools (using reference S288C). These are all the variants called by either tool that could be confirmed visually by aligning the reads to the reference in IGV (see Supplementary Fig. 1 for an example).
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