Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_3_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/20180503_oly_genome_pbjelly_sjw_01_bismark/ with the specified options: -q --score-min L,0,-0.2 -p 16 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	48376729
Number of alignments with a unique best hit from the different alignments:	15419326
Mapping efficiency:	31.9%
Sequences with no alignments under any condition:	13562727
Sequences did not map uniquely:	19394676
Sequences which were discarded because genomic sequence could not be extracted:	32144

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3436184	((converted) top strand)
CT/GA:	3414515	((converted) bottom strand)
GA/CT:	4287404	(complementary to (converted) top strand)
GA/GA:	4249079	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	92831596

Total methylated C's in CpG context:	12035424
Total methylated C's in CHG context:	405969
Total methylated C's in CHH context:	4939429
Total methylated C's in Unknown context:	2598

Total unmethylated C's in CpG context:	2449981
Total unmethylated C's in CHG context:	18062610
Total unmethylated C's in CHH context:	54938183
Total unmethylated C's in Unknown context:	17632

C methylated in CpG context:	83.1%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.2%
C methylated in Unknown context (CN or CHN):	12.8%


Bismark completed in 9d 23h 37m 31s