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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

idxMin countmafconseqcolreportDescription
11FALSEFALSEblackFALSECells with one variant are black.
21FALSETRUElight pinkTRUECells with one variant with high conseq are light pink.
31TRUEFALSEgreenFALSECells with one variant with MAF less than threshold are green.
41TRUETRUEdark magentaTRUECells with one variant with MAF less than threshold and high conseq are dark magenta.
52FALSEFALSEblueFALSECells with 2 or more variants are blue.
62FALSETRUEpinkTRUECells with 2 or more variants with high conseq in at least one are pink.
72TRUEFALSEredFALSECells with 2 or more variants with a MAF less than threshold in at least one are red.
82TRUETRUEcyanTRUECells 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