Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_7_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:	49730113
Number of alignments with a unique best hit from the different alignments:	16050504
Mapping efficiency:	32.3%
Sequences with no alignments under any condition:	13690949
Sequences did not map uniquely:	19988660
Sequences which were discarded because genomic sequence could not be extracted:	32535

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3651285	((converted) top strand)
CT/GA:	3630795	((converted) bottom strand)
GA/CT:	4389654	(complementary to (converted) top strand)
GA/GA:	4346235	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	97950003

Total methylated C's in CpG context:	13411305
Total methylated C's in CHG context:	439668
Total methylated C's in CHH context:	4998131
Total methylated C's in Unknown context:	2679

Total unmethylated C's in CpG context:	2579761
Total unmethylated C's in CHG context:	19668551
Total unmethylated C's in CHH context:	56852587
Total unmethylated C's in Unknown context:	18411

C methylated in CpG context:	83.9%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.1%
C methylated in Unknown context (CN or CHN):	12.7%


Bismark completed in 12d 6h 58m 3s