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


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