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Fig. 2 | BMC Bioinformatics

Fig. 2

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

Fig. 2

Screenshots of the output from Manhattan++ software. a) Transposed Manhattan plot on the left and lead variant annotation on the right. Alternating dark and light grey blocks represent the odd and even chromosomes respectively along the y-axis for those variants have association p-value greater than user-defined significance (5% False Discovery Rate). Blocks that contain variants with high impact and/or low MAF are highlighted using a bubble (eg 8). b) Zoomed in screenshot showing peak loci names in bubbles. c) The key showing the index (1–8), variant count (1, 2–200) in each block, annotation (MAF, impact, both), counter showing number of blocks in the plot for this index (eg. there are 2 blocks having index 8 on chromosomes 6 & 8). d) Zoomed in screenshot of a signal where there is a blue block (index 8) that could contain 2–200 variants with at least one variant having low MAF and high impact or two variants, one having low MAF and the other having high impact annotation

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