Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_16_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:	74531056
Number of alignments with a unique best hit from the different alignments:	22243864
Mapping efficiency:	29.8%
Sequences with no alignments under any condition:	20848664
Sequences did not map uniquely:	31438528
Sequences which were discarded because genomic sequence could not be extracted:	52465

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	5085546	((converted) top strand)
CT/GA:	5056511	((converted) bottom strand)
GA/CT:	6047871	(complementary to (converted) top strand)
GA/GA:	6001471	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	139396921

Total methylated C's in CpG context:	23216932
Total methylated C's in CHG context:	629407
Total methylated C's in CHH context:	6853423
Total methylated C's in Unknown context:	4650

Total unmethylated C's in CpG context:	3820019
Total unmethylated C's in CHG context:	27364516
Total unmethylated C's in CHH context:	77512624
Total unmethylated C's in Unknown context:	27879

C methylated in CpG context:	85.9%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.1%
C methylated in Unknown context (CN or CHN):	14.3%


Bismark completed in 7d 2h 3m 26s