rate my tophat2 results :-)

[duer777]

Hi,
New in RNA-seq and without any help in my lab, i would like to ask you your advice about my mapping results. (In my opinion, it's ok, but i will be very happy if experimented poeple can confirm it or not).
here are align summary tophat results and accepted_hits.bam analysed by samtool flagstat.

Left reads:
Input : 16641634
Mapped : 15985940 (96.1% of input)
of these: 4863655 (30.4%) have multiple alignments (7966 have >20)
Right reads:
Input : 16641634
Mapped : 15922959 (95.7% of input)
of these: 4834402 (30.4%) have multiple alignments (7972 have >20)
95.9% overall read mapping rate.

Aligned pairs: 15508899
of these: 4652618 (30.0%) have multiple alignments
87521 ( 0.6%) are discordant alignments
92.7% concordant pair alignment rate.

=============

47082928 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
47082928 + 0 mapped (100.00%:-nan%)
47082928 + 0 paired in sequencing
23593110 + 0 read1
23489818 + 0 read2
44621168 + 0 properly paired (94.77%:-nan%)
45651258 + 0 with itself and mate mapped
1431670 + 0 singletons (3.04%:-nan%)
2790766 + 0 with mate mapped to a different chr
86220 + 0 with mate mapped to a different chr (mapQ>=5)

Thanks for your advice.