samflag 0, what does it mean?

[capricy]

I tried to use tophat2.0.8 to map single end fasta reads to the genome,

tophat22.0.8 -o thout -N 1 <genome-index> <read.fasta>

and the results showed that samflags are 0 or 16, do they mean they are correctly mapped to the scaffold and reverse scaffold, respectively?

HWI-ST446:124987429:C0W8FACXX:6:1315:7610:23893 0 A_1 3390 50 65M * 0 0 CCTCACTACCATAACCAACTCCGAGATCCATTTGGAATGATCCGGGCTTGCTGCCACCGTCTGCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:65 YT:Z:UU NH:i:1

HWI-ST446:124987429:C0W8FACXX:6:2306:5526:62761 16 A_1 3291 50 65M * 0 0 TATCGTGAGGTTCACTGCTATATGGAGCGTACTGCCCATTATTCGCAATGCTACGATCAGCACAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0C64 YT:Z:UU NH:i:1



Thanks

[dpryan]

Yes. You may find this helpful (though it doesn't handle 0 very well).

[capricy]

Thank you very much for the reply

I knew that website. But, as you know, it does not tell anything about 0, so I would like confirm my guess...

[Brian Bushnell]

0 means a single-ended read is mapped to the plus strand with no abnormal flags set. If it is unmapped, the 4 bit will be set.