Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_17_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:	324236
Mapping efficiency:	32.4%
Sequences with no alignments under any condition:	253173
Sequences did not map uniquely:	422591
Sequences which were discarded because genomic sequence could not be extracted:	649

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	73296	((converted) top strand)
CT/GA:	72264	((converted) bottom strand)
GA/CT:	89778	(complementary to (converted) top strand)
GA/GA:	88249	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2014004

Total methylated C's in CpG context:	328054
Total methylated C's in CHG context:	8777
Total methylated C's in CHH context:	98157
Total methylated C's in Unknown context:	57

Total unmethylated C's in CpG context:	50630
Total unmethylated C's in CHG context:	428071
Total unmethylated C's in CHH context:	1100315
Total unmethylated C's in Unknown context:	398

C methylated in CpG context:	86.6%
C methylated in CHG context:	2.0%
C methylated in CHH context:	8.2%
C methylated in Unknown context (CN or CHN):	12.5%


Bismark completed in 0d 5h 26m 59s