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By checking the first graph "Empirical vs reported Phred score", we found reported base qualities are shifted to the right.
By checking the first graph "Empirical vs reported Phred score", we found reported base qualities are shifted to the right.
In this particular example, '33' was incorrectly added to all base qualities.
In this particular example, '33' was incorrectly added to all base qualities. Such data used in variant calling may increase false positive SNP calling.
When such data used in variant calling, we may increase false positive SNP variants.
