Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_11_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:	54458572
Number of alignments with a unique best hit from the different alignments:	16320566
Mapping efficiency:	30.0%
Sequences with no alignments under any condition:	15053965
Sequences did not map uniquely:	23084041
Sequences which were discarded because genomic sequence could not be extracted:	40206

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3664176	((converted) top strand)
CT/GA:	3633017	((converted) bottom strand)
GA/CT:	4511175	(complementary to (converted) top strand)
GA/GA:	4471992	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	104048121

Total methylated C's in CpG context:	18520646
Total methylated C's in CHG context:	492903
Total methylated C's in CHH context:	5003405
Total methylated C's in Unknown context:	3654

Total unmethylated C's in CpG context:	2984829
Total unmethylated C's in CHG context:	20797118
Total unmethylated C's in CHH context:	56249220
Total unmethylated C's in Unknown context:	21750

C methylated in CpG context:	86.1%
C methylated in CHG context:	2.3%
C methylated in CHH context:	8.2%
C methylated in Unknown context (CN or CHN):	14.4%


Bismark completed in 2d 20h 46m 16s