Detection of polymorphisms from Escherichia coli NGS by PED

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In this section, install of Linux(Ubuntu), setup of PED and browsing of detected polymorphisms using NGS of mutant strains of Escherichia coli str. K-12 substr. MG1655 are described.

An example of genome view by IGV. Click to large. Strain CAG67106 (SRR11791057) is a suppressor mutant of mreB mutation.
Mutation at 4,181,702 is C to T substitution (P153L) in the RpoB gene.

Install of Ubuntu

Setup and analysis of PED

For Docker users

Visualization of detected polymorphisms using IVG

Link of PED

Contact

MIYAO Akio, Ph.D (miyao@affrc.go.jp) (Family name is MIYAO)
Institute of Crop Science / NARO
2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan