Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_18_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:	55048106
Number of alignments with a unique best hit from the different alignments:	18869098
Mapping efficiency:	34.3%
Sequences with no alignments under any condition:	14051321
Sequences did not map uniquely:	22127687
Sequences which were discarded because genomic sequence could not be extracted:	37148

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	4120413	((converted) top strand)
CT/GA:	4097029	((converted) bottom strand)
GA/CT:	5326285	(complementary to (converted) top strand)
GA/GA:	5288223	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	113572211

Total methylated C's in CpG context:	14713606
Total methylated C's in CHG context:	443442
Total methylated C's in CHH context:	5621164
Total methylated C's in Unknown context:	2746

Total unmethylated C's in CpG context:	2907663
Total unmethylated C's in CHG context:	23410658
Total unmethylated C's in CHH context:	66475678
Total unmethylated C's in Unknown context:	19896

C methylated in CpG context:	83.5%
C methylated in CHG context:	1.9%
C methylated in CHH context:	7.8%
C methylated in Unknown context (CN or CHN):	12.1%


Bismark completed in 8d 6h 34m 2s