I'm looking at my gigaBayes output, for which I've specified --o 3 so that I get individual allele counts, but not listings of each read. I'm getting a sub-field in the 9th column of the gff output that looks like this:
individualAlleleCounts=MID11:T|1|40|+|1|40|-|0|0&C|0|0|+|0|0|-|0|0,MID9:T|0|0|+|0|0|-|0|0&C|1|40|+|1|40|-|0|0
... but the manual only illustrates this field like so:
individualAlleleCounts=Person1:G|4|120&A|1|30,Person2:G|2|60&A|2|60
So, I understand that my results indicate, for individual "MID11", one read with a "T" base at this position, with base quality = 40. But what are the "+|1|40|-|0|0" fields ...? Sometimes they have positive values after the "+", and sometimes after the "-" ... and I don't see these "+" or "-" fields in the example output, nor can I find an explanation in the manual.
Does anyone know what these fields mean? I'm concerned that I'm missing something that gigaBayes is trying to tell me ...
~Joe
individualAlleleCounts=MID11:T|1|40|+|1|40|-|0|0&C|0|0|+|0|0|-|0|0,MID9:T|0|0|+|0|0|-|0|0&C|1|40|+|1|40|-|0|0
... but the manual only illustrates this field like so:
individualAlleleCounts=Person1:G|4|120&A|1|30,Person2:G|2|60&A|2|60
So, I understand that my results indicate, for individual "MID11", one read with a "T" base at this position, with base quality = 40. But what are the "+|1|40|-|0|0" fields ...? Sometimes they have positive values after the "+", and sometimes after the "-" ... and I don't see these "+" or "-" fields in the example output, nor can I find an explanation in the manual.
Does anyone know what these fields mean? I'm concerned that I'm missing something that gigaBayes is trying to tell me ...
~Joe
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