Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_9_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:	346612
Mapping efficiency:	34.7%
Sequences with no alignments under any condition:	242736
Sequences did not map uniquely:	410652
Sequences which were discarded because genomic sequence could not be extracted:	674

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	76661	((converted) top strand)
CT/GA:	76331	((converted) bottom strand)
GA/CT:	97008	(complementary to (converted) top strand)
GA/GA:	95938	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2052482

Total methylated C's in CpG context:	232563
Total methylated C's in CHG context:	7170
Total methylated C's in CHH context:	97165
Total methylated C's in Unknown context:	62

Total unmethylated C's in CpG context:	54861
Total unmethylated C's in CHG context:	402828
Total unmethylated C's in CHH context:	1257895
Total unmethylated C's in Unknown context:	337

C methylated in CpG context:	80.9%
C methylated in CHG context:	1.7%
C methylated in CHH context:	7.2%
C methylated in Unknown context (CN or CHN):	15.5%


Bismark completed in 0d 8h 40m 21s