Bismark report for: MoPh11_1.fq.gz and MoPh11_2.fq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /media/eternus1/nfs/projects/dpanchenko/komarek/ChiPseq/bismark_genome/ with the specified options: -q --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	360304377
Number of paired-end alignments with a unique best hit:	179079085
Mapping efficiency:	49.7% 
Sequence pairs with no alignments under any condition:	170129878
Sequence pairs did not map uniquely:	11095414
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	89561929	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	89517155	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
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Total number of C's analysed:	11115474037

Total methylated C's in CpG context:	495263726
Total methylated C's in CHG context:	14692763
Total methylated C's in CHH context:	38906317
Total methylated C's in Unknown context:	47616

Total unmethylated C's in CpG context:	252761807
Total unmethylated C's in CHG context:	2610019985
Total unmethylated C's in CHH context:	7703829439
Total unmethylated C's in Unknown context:	3903476

C methylated in CpG context:	66.2%
C methylated in CHG context:	0.6%
C methylated in CHH context:	0.5%
C methylated in Unknown context (CN or CHN):	1.2%


Bismark completed in 0d 7h 23m 11s