Bismark report for: MoPh7_1.fq.gz and MoPh7_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:	360143930
Number of paired-end alignments with a unique best hit:	285213251
Mapping efficiency:	79.2% 
Sequence pairs with no alignments under any condition:	56550783
Sequence pairs did not map uniquely:	18379896
Sequence pairs which were discarded because genomic sequence could not be extracted:	7

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	142596084	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	142617160	((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:	16207910024

Total methylated C's in CpG context:	547302172
Total methylated C's in CHG context:	20181839
Total methylated C's in CHH context:	60009493
Total methylated C's in Unknown context:	58521

Total unmethylated C's in CpG context:	304191885
Total unmethylated C's in CHG context:	3541798079
Total unmethylated C's in CHH context:	11734426556
Total unmethylated C's in Unknown context:	5468981

C methylated in CpG context:	64.3%
C methylated in CHG context:	0.6%
C methylated in CHH context:	0.5%
C methylated in Unknown context (CN or CHN):	1.1%


Bismark completed in 0d 8h 41m 44s