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Table 1 Relevant columns in the configuration file for the software

From: Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers

idx

Min count

maf

conseq

col

report

Description

1

1

FALSE

FALSE

black

FALSE

Cells with one variant are black.

2

1

FALSE

TRUE

light pink

TRUE

Cells with one variant with high conseq are light pink.

3

1

TRUE

FALSE

green

FALSE

Cells with one variant with MAF less than threshold are green.

4

1

TRUE

TRUE

dark magenta

TRUE

Cells with one variant with MAF less than threshold and high conseq are dark magenta.

5

2

FALSE

FALSE

blue

FALSE

Cells with 2 or more variants are blue.

6

2

FALSE

TRUE

pink

TRUE

Cells with 2 or more variants with high conseq in at least one are pink.

7

2

TRUE

FALSE

red

FALSE

Cells with 2 or more variants with a MAF less than threshold in at least one are red.

8

2

TRUE

TRUE

cyan

TRUE

Cells with 2 or more variants with at least one variant with MAF less than threshold and at least one variant with the conseq flag are cyan.

  1. Each display cell shows two annotation features (MAF & consequence (conseq)). Report column instructs the code whether a bubble is drawn on the plot (Fig. 2d). These are features of interest like low MAF or high consequence or both. Reporting of bubbles take place on cells which are above the FDR threshold (Fig. 2a). Rest of the cells are alternating dark and light grey blocks represent the odd and even chromosomes respectively. Min.count contains the minimum number of variants in each cell. First 4 rows show configuration for cells with one variant. The next 4 rows are for cells that contain 2 or more variants