Why alignment of sequence reads to a reference can be inaccurate towards the ends of a read

Question

[freeheart.steven]

I often heard that "alignment of sequence reads to a reference can be inaccurate towards the ends of a read", does anybody know the exact reason of this?

[Brian Bushnell]

Cross-posted on SeqAnswers

Answer 1

[GouthamAtla]

One reason would be that the quality of the reads gets dropped at the end. Its because of the sequencing chemistry.

Hence for e.g, a 100 bp read will have low quality bases at the end (10-20 bases). Its good to see the box plot of quality score and trim off the bases if necessary before alignment.

[lakhujanivijay]

Why quality of the reads gets dropped at the end?