Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_12_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:	59459431
Number of alignments with a unique best hit from the different alignments:	20890554
Mapping efficiency:	35.1%
Sequences with no alignments under any condition:	15643544
Sequences did not map uniquely:	22925333
Sequences which were discarded because genomic sequence could not be extracted:	37887

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	4663862	((converted) top strand)
CT/GA:	4630478	((converted) bottom strand)
GA/CT:	5799691	(complementary to (converted) top strand)
GA/GA:	5758636	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	124396429

Total methylated C's in CpG context:	14492989
Total methylated C's in CHG context:	455769
Total methylated C's in CHH context:	6351378
Total methylated C's in Unknown context:	2695

Total unmethylated C's in CpG context:	3513867
Total unmethylated C's in CHG context:	25149482
Total unmethylated C's in CHH context:	74432944
Total unmethylated C's in Unknown context:	21222

C methylated in CpG context:	80.5%
C methylated in CHG context:	1.8%
C methylated in CHH context:	7.9%
C methylated in Unknown context (CN or CHN):	11.3%


Bismark completed in 3d 14h 28m 32s