Fastq file download from pubmed

Question

[mikysyc2016]

Hi all, I download a sra file from pubmed and transfer it to fastq, but when i open it, the file is weird.please see below:

@SRR653007.1 ILLUMINA-8879DC:227:2:1:1030:943:0:1 length=35
NTGACTGGATGCCTGGGTTGATGCTGTTGTTATTT
+SRR653007.1 ILLUMINA-8879DC:227:2:1:1030:943:0:1 length=35
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@SRR653007.2 ILLUMINA-8879DC:227:2:1:1063:946:0:1 length=35
NATTGTGTTTTTCTCATTTTCCGTAATTTTCAGTT
+SRR653007.2 ILLUMINA-8879DC:227:2:1:1063:946:0:1 length=35
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@SRR653007.3 ILLUMINA-8879DC:227:2:1:1102:948:0:1 length=35
NGGTTCAGATCATCTGCACAGGTCACGTCAGCCCT

I do not know whether the %%%%%% will effect the analysis. Can i get your suggestion? Thanks

[JC]

Nothing is wrong with your file, it's a Fastq file which encodes the nucleotidic sequence and their quality, the "%" is a low-quality value in Phred+33 scale. Check https://en.wikipedia.org/wiki/FASTQ_format

[mikysyc2016]

I also download other sra file, they are look like common. Thank you for your reply. Does that mean the some part of the file quality is not good enough?

[GenoMax]

You can draw no useful conclusions by looking at a few reads out of possible millions in a file. Go ahead and do some proper QC/analysis.

[WouterDeCoster]

I download a sra file from pubmed

That's a bit unlikely. Pubmed doesn't have sra files, but is a database of academic literature.

SRA has sra files.

[ATpoint]

Before digging deeper into this: What is the question you want to answer, what kind of data is this and most importantly, why do you find the % qualities strange? Are you familiar with fastq files in general?