Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_1_s456_trimmed.fq.gz (version: v0.19.1)
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
Bismark was run with Bowtie 2 against the bisulfite genome of /home/sam/data/oly_methylseq/oly_genome/ with the specified options: -q --score-min L,0,-0.2 -p 16 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	1000000
Number of alignments with a unique best hit from the different alignments:	330105
Mapping efficiency:	33.0%
Sequences with no alignments under any condition:	262553
Sequences did not map uniquely:	407342
Sequences which were discarded because genomic sequence could not be extracted:	686

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	73370	((converted) top strand)
CT/GA:	72888	((converted) bottom strand)
GA/CT:	91956	(complementary to (converted) top strand)
GA/GA:	91205	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2004225

Total methylated C's in CpG context:	268177
Total methylated C's in CHG context:	8942
Total methylated C's in CHH context:	100991
Total methylated C's in Unknown context:	53

Total unmethylated C's in CpG context:	55344
Total unmethylated C's in CHG context:	401993
Total unmethylated C's in CHH context:	1168778
Total unmethylated C's in Unknown context:	383

C methylated in CpG context:	82.9%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.0%
C methylated in Unknown context (CN or CHN):	12.2%


Bismark completed in 0d 6h 5m 49s