Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_8_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:	38697189
Number of alignments with a unique best hit from the different alignments:	12575055
Mapping efficiency:	32.5%
Sequences with no alignments under any condition:	10453397
Sequences did not map uniquely:	15668737
Sequences which were discarded because genomic sequence could not be extracted:	25167

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2775397	((converted) top strand)
CT/GA:	2761832	((converted) bottom strand)
GA/CT:	3516452	(complementary to (converted) top strand)
GA/GA:	3496207	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	76972639

Total methylated C's in CpG context:	11089716
Total methylated C's in CHG context:	334631
Total methylated C's in CHH context:	3887465
Total methylated C's in Unknown context:	2216

Total unmethylated C's in CpG context:	1652203
Total unmethylated C's in CHG context:	15523342
Total unmethylated C's in CHH context:	44485282
Total unmethylated C's in Unknown context:	14395

C methylated in CpG context:	87.0%
C methylated in CHG context:	2.1%
C methylated in CHH context:	8.0%
C methylated in Unknown context (CN or CHN):	13.3%


Bismark completed in 12d 18h 13m 11s