Fig. 2

An example on how to construct input features for an indel candidate site. a Reference sequence and read pileup at the candidate site before and after multiple sequence alignment, and the consensus sequence. b Reference sequence and consensus sequence at the candidate site before and after pairwise alignment, and the inferred sequence. c Raw counts of each symbol at each column of multiple sequence alignment pileup. d Matrix M, showing frequency of each symbol at each column of multiple sequence alignment pileup. e First channel of input image, matrix M minus Q (one-hot encoding of realigned reference sequence). f Matrix Q, one-hot encoding of realigned reference sequence which forms the second channel of input image for NanoCaller deep convolutional neural network