Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/3_TTAGGC_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:	11555321
Number of alignments with a unique best hit from the different alignments:	4558848
Mapping efficiency:	39.5%
Sequences with no alignments under any condition:	1568078
Sequences did not map uniquely:	5428395
Sequences which were discarded because genomic sequence could not be extracted:	8921

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2082412	((converted) top strand)
CT/GA:	2076802	((converted) bottom strand)
GA/CT:	194744	(complementary to (converted) top strand)
GA/GA:	195969	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	25864841

Total methylated C's in CpG context:	1008114
Total methylated C's in CHG context:	77277
Total methylated C's in CHH context:	1449502
Total methylated C's in Unknown context:	404

Total unmethylated C's in CpG context:	2566173
Total unmethylated C's in CHG context:	4698459
Total unmethylated C's in CHH context:	16065316
Total unmethylated C's in Unknown context:	4356

C methylated in CpG context:	28.2%
C methylated in CHG context:	1.6%
C methylated in CHH context:	8.3%
C methylated in Unknown context (CN or CHN):	8.5%


Bismark completed in 0d 10h 44m 9s