Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_11_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/oly_genome/ with the specified options: -q --score-min L,0,-0.2 -p 16 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	1000000
Number of alignments with a unique best hit from the different alignments:	304722
Mapping efficiency:	30.5%
Sequences with no alignments under any condition:	264364
Sequences did not map uniquely:	430914
Sequences which were discarded because genomic sequence could not be extracted:	784

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	67566	((converted) top strand)
CT/GA:	66740	((converted) bottom strand)
GA/CT:	84908	(complementary to (converted) top strand)
GA/GA:	84724	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1943271

Total methylated C's in CpG context:	346776
Total methylated C's in CHG context:	8887
Total methylated C's in CHH context:	91070
Total methylated C's in Unknown context:	73

Total unmethylated C's in CpG context:	55685
Total unmethylated C's in CHG context:	389558
Total unmethylated C's in CHH context:	1051295
Total unmethylated C's in Unknown context:	366

C methylated in CpG context:	86.2%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.0%
C methylated in Unknown context (CN or CHN):	16.6%


Bismark completed in 0d 3h 32m 21s