Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_4_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:	44905078
Number of alignments with a unique best hit from the different alignments:	14481141
Mapping efficiency:	32.2%
Sequences with no alignments under any condition:	12422799
Sequences did not map uniquely:	18001138
Sequences which were discarded because genomic sequence could not be extracted:	29863

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3213378	((converted) top strand)
CT/GA:	3191749	((converted) bottom strand)
GA/CT:	4034139	(complementary to (converted) top strand)
GA/GA:	4012012	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	88412183

Total methylated C's in CpG context:	12356131
Total methylated C's in CHG context:	405585
Total methylated C's in CHH context:	4601291
Total methylated C's in Unknown context:	2308

Total unmethylated C's in CpG context:	1987938
Total unmethylated C's in CHG context:	17770448
Total unmethylated C's in CHH context:	51290790
Total unmethylated C's in Unknown context:	16328

C methylated in CpG context:	86.1%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.2%
C methylated in Unknown context (CN or CHN):	12.4%


Bismark completed in 10d 12h 38m 11s