- The NH tag is exported.
- The NM tag is not exported.
- The workbench exports color space information in the CS tag.
- The colors of a right mate are incorrect since the colors of a paired read are stored as a single color string.
- For hard clipped sequence reads, the color space is incorrect, since the color space string is not hard clipped.
- SAM files contain sequence quality score and color quality
scores. The workbench only have color quality scores and these are
stored and exported as sequence quality scores.