Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/5_ACAGTG_L001_R1_001_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:	12231319
Number of alignments with a unique best hit from the different alignments:	4798520
Mapping efficiency:	39.2%
Sequences with no alignments under any condition:	1651146
Sequences did not map uniquely:	5781653
Sequences which were discarded because genomic sequence could not be extracted:	9631

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2187003	((converted) top strand)
CT/GA:	2186040	((converted) bottom strand)
GA/CT:	207926	(complementary to (converted) top strand)
GA/GA:	207920	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	27207691

Total methylated C's in CpG context:	1043108
Total methylated C's in CHG context:	84105
Total methylated C's in CHH context:	1546253
Total methylated C's in Unknown context:	435

Total unmethylated C's in CpG context:	2688305
Total unmethylated C's in CHG context:	4955714
Total unmethylated C's in CHH context:	16890206
Total unmethylated C's in Unknown context:	4529

C methylated in CpG context:	28.0%
C methylated in CHG context:	1.7%
C methylated in CHH context:	8.4%
C methylated in Unknown context (CN or CHN):	8.8%


Bismark completed in 0d 18h 32m 9s