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Old 04-13-2011, 03:03 AM   #1
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Location: India

Join Date: Mar 2011
Posts: 4
Default fastq quality values

Hi All,
We have a couple of questions related to the fastq format and quality values:
1. We have been looking at the quality values of the base 'N' which is essentially an ambiguous base. For such a base, what is the interpretation of its quality value in the fastq file?
2. In some fastq files we have observed that the quality values for base 'N" take a range of values say ASCII 33-40. In these files we have also noticed that some other 'non-ambiguous' bases (which are not N and could be any of A, T, C anf G) have quality values in the same range? In fact some 'N's have a higher quality value that some A, T, C and G! How is this possible? We are trying to understand the meaning of the quality value of N. In such a case, would it make sense to retain the quality values of N?
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base calling, fastq quality numbers

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