Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_6_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:	46455148
Number of alignments with a unique best hit from the different alignments:	16197809
Mapping efficiency:	34.9%
Sequences with no alignments under any condition:	12629511
Sequences did not map uniquely:	17627828
Sequences which were discarded because genomic sequence could not be extracted:	28969

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3590424	((converted) top strand)
CT/GA:	3574446	((converted) bottom strand)
GA/CT:	4517598	(complementary to (converted) top strand)
GA/GA:	4486372	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	94305654

Total methylated C's in CpG context:	9507171
Total methylated C's in CHG context:	406569
Total methylated C's in CHH context:	5152555
Total methylated C's in Unknown context:	2031

Total unmethylated C's in CpG context:	2409490
Total unmethylated C's in CHG context:	18493047
Total unmethylated C's in CHH context:	58336822
Total unmethylated C's in Unknown context:	16126

C methylated in CpG context:	79.8%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.1%
C methylated in Unknown context (CN or CHN):	11.2%


Bismark completed in 11d 16h 35m 19s