Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_7_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:	327795
Mapping efficiency:	32.8%
Sequences with no alignments under any condition:	264497
Sequences did not map uniquely:	407708
Sequences which were discarded because genomic sequence could not be extracted:	671

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	74004	((converted) top strand)
CT/GA:	73152	((converted) bottom strand)
GA/CT:	90381	(complementary to (converted) top strand)
GA/GA:	89587	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2002393

Total methylated C's in CpG context:	275174
Total methylated C's in CHG context:	8721
Total methylated C's in CHH context:	99298
Total methylated C's in Unknown context:	54

Total unmethylated C's in CpG context:	52432
Total unmethylated C's in CHG context:	404434
Total unmethylated C's in CHH context:	1162334
Total unmethylated C's in Unknown context:	405

C methylated in CpG context:	84.0%
C methylated in CHG context:	2.1%
C methylated in CHH context:	7.9%
C methylated in Unknown context (CN or CHN):	11.8%


Bismark completed in 0d 8h 1m 31s