Unusual indel peaks in bam file

Question

[boczniak767]

HI,

I'm reanalysing project GSE124340 (RNA-seq).

Quality control of input fastq's with FastQC haven't detected any problems however after alignment I've got indel frequencies in BamQC like this.

I've used STAR aligner: the command used in loop

~/bin/STAR_2.7.10b/Linux_x86_64/STAR --runThreadN 24 --readFilesIn ${srr}_1.fastq.gz ${srr}_2.fastq.gz \
--genomeDir /media/mj/bb71e88b-2122-487c-a602-a2552c680021/star-index --outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix ${srr} --readFilesCommand zcat`

So I've used default settings. Also The data is from the reference genome (B73 reads aligned to B73 genome) and I've not seen such peaks in several other project I've analysed.

Should I try to remove this effect (how?) or it is safe to procceed?