For past two hours I tried to browse around for samtools flagstat output information, unfortunately could not find much related to my problem - this is my samtool flagstat output for single end reads - does anyone think that the tophat alignment did not work well. Please let me know. Any possible replies would be greatly appreciated. Thanks in advance.
$ samtools flagstat accepted_hits.bam
18109074 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 18109074 + 0 mapped (100.00%:nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (nan%:nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (nan%:nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)