I am having difficulty navigating all of the considerations when thinking about strand-specific sequencing, and how to determine which actual strand a read comes from.

Here is the setup: I have paired-end Illumina sequence generated with a strand-specific library. It was put through Tophat using the first-strand option, and now I have a SAM file. While browsing the SAM file, I see my read pairs and am interpreting their flag stat, but my mind is going in circles trying to determine if the pair mapped to the actual (+) or (-) strand, which I need to know for distinguishing counts in cases of overlapping genes. I realize that reads spanning junctions have the XS field, but I want to find strandedness from just the flag stat.

Consider 3 pairs of reads that are properly paired in mapping:

READ_ID_A       99      Chr1    155388  50      76M     =       155531  219     TTCAGCTTCTTTGAATCTCTTGACGTTGTGTAGAAGCCATTTGTATGATTCATCTTTTCGGTCTTGACACGGATCG
READ_ID_A       147     Chr1    155531  50      76M     =       155388  -219    CACACGACACCGTTTCGTCTAGCTTCGGCAAGTGAAGCAGAAACGTGAGGACGTTGGCATTTGATGCATAGAAAAT


READ_ID_B       99      Chr1    180537  50      76M     =       180672  211     TGCGCTTGTGGTTGATCTTTCTTCTCTCCTTCCTTCTTATCGCCACCTTCTTTCTTCTCTTCTTCCTTCTTCGGTG
READ_ID_B       147     Chr1    180672  50      76M     =       180537  -211    CCACCACCTTCCTTCTTCGGCTCCTCCTTCTTCTCCTTTTCCGGCTCTTTCGCAGGTCCCACTAGTACGATATCCG


READ_ID_C       163     Chr1    285419  50      75M     =       285474  130     GGCTACTATGGCCCTGTCTCTGGCTGAAGCTAGGCTTCAGGTTATAGTGGAATCACTTGAAGCTGGTGCAGGGAA
READ_ID_C       83      Chr1    285474  50      75M     =       285419  -130    CTTGAAGCTGGTGCAGGGAATGATATTCCACATGTGTCTGAAGAGACTGAGGAAACAATAGATGTTAATGATAAA

Looking at just the first two reads in READ_ID_A, we can decipher the flag stat to find out that the first read is R1, and is from the (-) strand. Likewise, the second read is R2, and is from the (+) strand.

For READ_ID_B, the first read is R1 and (-), and the second is R2 and (+).

However, for READ_ID_C, the first read is R2 (-) and the second is R1 (+).

So, from this information, how can I tell which of these pairs of reads should be assigned to the (+) or (-) strand of the reference genome? I was thinking perhaps I should just check the strandedness of R1, and use that. So, if R1 turns out to be (+), then I will assign the R1/R2 pair to the (+) of the reference. Is this wrong?

EDIT: Perhaps I interpreted the flag stat incorrectly? Does anyone reach the same conclusion as me?