Question about SAM files columns

Question

[mangfu100]

Hi

I am doing sequencing using sam files.

but there is one thing that i didn't understand about sam field.

For example, one of my sam file read is below.

HWI-ST478:409:D1R9FACXX:4:2301:17848:28448      163     10      243428  60      101M    =       243830  503

A first read position is 243428 and the second read position 243830. So first read is before the second read.

and I also find that first read is second section in pair by doing bitwise col2 which is 163.

consider the two things above that i mention (bold text) , I can draw the paired end read like this.

   -----------                                   -------------  (paired end reads with insert size)
243830 (first section in pair)           243428(second section in pair)

but it is contradiction.. because first read that has position 243428 is after the second read but its positions number is different direction.

So I conclude that the first,second section is just a meaningless number.

Is it right?

Answer 1

[Devon Ryan]

First and second refer to mate 1 and 2 in sequencing (or the first and second read in a pair, if you prefer that phrasing) and have nothing to do with their relative positions or order in the resulting alignment.

So you have:

            <-----read1
read2---->