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week 7 Determination of major and minor mutations in sequencing data from…
week 7 Determination of major and minor mutations in sequencing data from mixed infections
understand the concept of mixed infections
What is a mixed infection?
species 1 strain A - species 1 strain B: A Mixed strain infection
Species 1 - species 2 known as: Mixed species infection
Example: Malaria
p. malariae
p.vivax
P. falciparum
p.ovale
p.knowlesi
Covid variants
Pcr vs sequencing
Types
Beta (b.1.351, South Africa)
Gamma (p.1, Brazil)
Delta (b.1.617.2, India)
Omicron (b.1.1.529, South Africa)
Wild Type (WT)
Alpha (b.1.1.7, UK)
Majority and minority variants
Minority: triangles and squares (3)
often we only report the majority variant as identified variant
Majority: circles (4)
Understand the concepts of major and minor variants
Why are minor variants important
Sustained growth in a minor variant could mean enhanced functionality
Allows for tracing of variants prior to them becoming public health challenges
Every variant was at some point a minor variant
Understand how to calculate relevant variant statistics from KMA
output files
Exercise
Become familiar with the VCF format
VCF DP, AD, AF, RAF, AD6
DP=2841;AD=2310;AF=0.81;RAF=0.81;DEL=219;
AD6=32,2310,9,271,0,219
BEAST