Hi,

A gene is always oriented from 5' to 3'. Your first position (349603) is a larger number than the second position. Therefore, your gene of interest should be located on the reverse strand.

There are some other formats like GFF3 which will always list the smaller number first. However, such formats include an additional column to indicate the orientation (+/-) of the feature.

hi

for each chromosome, from the beginning to the end, following the 5'3' orientation on the + strand, it's given from p to q.

fred

The genomic coordinates are given and queried from the lowest to the highest, irrespective of gene direction. Check this example in the UCSC genome browser hg38: chr9:133,328,774-133,336,398 for SURF6. Best.

You need to correlate the genomic coordinates with your read coordinates (do not forget from each pair the read refers to) and compare their orientation.