Output format

accuMUlate generates a table of results, which includes information for every site with a mutation probability greater that the value set by the -p option (which defaults to 0.1). The file is tab-delimited (so can be read into R with read.table or pandas with read_table) and the first three columns are the chromosome, start and end position of putative mutations. This latter property means the file can be used as a bed file, including as input to the --intervals argument of accumulate itself.

The rest of file contains summary information about each putative mutation. This includes the probability that a given site is a mutation according to our model, and other statistics that may help to filter out false positives introduced by sequencing error, poorly mapped reads or aberations during library preparation. The contents of each column is described below, a more complete summary of each statistic is provided here.

Column	Content	Note
1	Chromosome	The first three columns represent the position of a putative mutation in bed format.
2	Bed interval start
3	Bed interval end
4	Reference allele
5	Mutant sample	Most probably mutant sample at this site
6	Mutation direction	Most probable mutation at this site, from ancestral to descendant genotype
7	Probability of a mutation	Estimated probability of at least one mutation at this site
8	Probability of one mutation	Estimated probability of exactly one mutation at this site
9	Probability of correct descendant genotype	Akin to a genotype quality score -- probability of the mutation direction above being correct
10	Likelihood	Overall likelihood for this site
11	Depth	Number of mapped-bases passing filtering criteria across all samples
12	FWD reads that contain the mutation	Number of reads in FWD orientation that support the mutation in the mutant site
13	REV reads that contain the mutation	Number of reads in REV orientation that support the mutation in the mutant site
14	N. ancestral in mutant	Number of reads for a non-mutant allele in the mutant sample (note: you may expect many such reads in a diploid->diploid experiment).
15	N. mutant in wt	Number of reads matching the putatively-mutant allele in samples that are not mutants
16	Mapping quality difference	AD test statistic for a difference in mapping quality between mutant and non-mutant alleles
17	Insert Size difference	AD test statistic for a difference in inferred insert size between mutant and non-mutant alleles
18	Stand Bias	p-value from a Fisher's exact test of stand bias between mutant and non-mutant alleles
19	Pair-mapping rate difference	p-value from a Fisher's exact test examining whether read-pairs map more frequently between mutant and non-mutant alleles.