why the read sequence from IGV can't be found in fastq?

[maubp]

My guess is the sequence has been reverse complemented, and that's why you can't find it. As dpryan suggests, try searching by the read name instead.

[dpryan]

Try grepping for the read name, that's less error prone:

zgrep -A 3 "HWI:stuff" file.fastq.gz

[hujiacun]

I found a strange read pair from IGV, so i want to extract the original information about the read pair.
I use " zcat file.fastq.gz | grep -B 3 "TCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCCAAGGATCTACATATGATCAAAACATATCTTTACCAGATTCTCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTGATC"
The strange thing is i can't find it in original fq file.