TopHat SAM file error

[shurjo]

Hi,

A recent paired-end TopHat run on my data created SAM files with a error I have not seen before: for the two pairs, even if the best match is found on different chromosomes, field 7 in the Alignment section (MRNM) has the value "=", which should be true only if they were on the same chromosome. I am pasting an example below, where the two PE mates map to chr1 and chrX.

42RFMAAXX:2:089:0997:0562       177     chr1    225935280       255     51M     =       114953101       0       ATAACACTCCAATACCACTTTGTTGTCAGTGTAAACAAGGGCATATCCCGG  >=?>B9@?@ABBA>B?=BAA9AB>AB9BB@B?CC@=CBBBCB?@:BA>@>B      NM:i:2
42RFMAAXX:2:089:0997:0562       113     chrX    114953101       255     51M     =       225935280       0       TTGACATTGTCTCTCTTTTTGACTTTCCTTTTGCCTCTGTCTCTTCCTCAC  B@>?C?B?BBCBBBCB?B:AB?BBA<@BBAABABBB@CA@B@CBBC@BB?B      NM:i:1

Has anyone encountered this before?

Thanks,

Shurjo