I have performed GATK's Base Quality Score Recalibration (BQSR) on my BAM files. 

The BQSR has made the per base sequence quality look very bad on FastQC. Is this normal? Should I use the BAM files that have been through BQSR and therefore have worse FastQC reports?

The FastQC per base sequence quality goes from being in the green zone ![https://ibb.co/hyv5DQy][1] 

to being all in the lower red zone 

![https://ibb.co/ckN1fFw][2] 

The next step I will do is SNP calling. This is genomic data.

(The BAM files contain only the data that is paired, matches uniquely, and has the duplicates marked by Picard). The FastQC images are from just one of my samples but all samples have the same pattern of being all green or almost all in the green zone, to being entirely in the red zone after BQSR.


  [1]: https://i.ibb.co/g3C1zq3/Screenshot-2019-06-12-at-10-19-19.png
  [2]: https://i.ibb.co/hLKyQWc/Screenshot-2019-06-12-at-10-19-30.png
Apparently it is because I only have data for 1 gene and GATK says "A critical determinant of the quality of the recalibration is the number of observed bases and mismatches in each bin. This procedure will not work well on a small number of aligned reads. We usually expect to see more than 100M bases per read group; as a rule of thumb, larger numbers will work better" https://software.broadinstitute.org/gatk/documentation/article?id=11081 