That does make sense - if the aligner is error prone around the exon/intron boundaries it wouldn't be surprising to see a higher error rate.
And yes, mismatch and indel are taken to be distinct in this case - a mismatch is a base that is aligned to a reference base but does not match, which by definition is mutually exclusive with indels.
-t
On Feb 23, 2012, at 1:07 PM, Richard Corbett wrote:
> Aha,
> So if my reads are RNAseq and have frequent gaps for introns then seeing a number like .5 in the mismatch rate may not be so bad.
>
> Are the mismatch rate and Indel rate mutually exclusive meaning the indels are not considered mismatches and vice versa?
>
> thanks,
> Richard
>
>
> On 02/23/2012 09:56 AM, Tim Fennell wrote:
>> The numbers are calculated by using the basecalls from the read, and the cigar string to match up the read bases with the appropriate reference bases and then calculate the fraction which mismatch the reference (we include in this read bases which are no-calls).
>>
>> The PF_MISMATCH_RATE is simply the number of mismatching aligned bases divided by all aligned bases.
>>
>> The PF_HQ_ERROR_RATE is perhaps poorly named, but is the same calculation as above except that it only looks at reads with a mapping quality of 20 or higher
>>
>> PF_INDEL_RATE is the number of insertion or deletion events per 100 read bases.
>>
>> -t
>>
>> On Feb 23, 2012, at 12:46 PM, Richard Corbett wrote:
>>
>>> Hi all,
>>>
>>> Does anyone know how these numbers are calculated? ie, are they based on
>>> flags, the cigar, or sequence string?
>>>
>>> PF_MISMATCH_RATE 0.47867 0.476719 0.477708
>>> PF_HQ_ERROR_RATE 0.48216 0.481005 0.481589
>>> PF_INDEL_RATE 0.00009 0.000095 0.000093
>>>
>>> Also, a question about interpretation... is this telling me that .477
>>> percent of my aligned bases are mismatch errors?
>>>
>>> thanks,
>>> RIchard
>>>
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