Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/6_GCCAAT_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/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:	395712
Mapping efficiency:	39.6%
Sequences with no alignments under any condition:	129226
Sequences did not map uniquely:	475062
Sequences which were discarded because genomic sequence could not be extracted:	838

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	179691	((converted) top strand)
CT/GA:	180213	((converted) bottom strand)
GA/CT:	17490	(complementary to (converted) top strand)
GA/GA:	17480	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2235158

Total methylated C's in CpG context:	82834
Total methylated C's in CHG context:	7846
Total methylated C's in CHH context:	129683
Total methylated C's in Unknown context:	39

Total unmethylated C's in CpG context:	223364
Total unmethylated C's in CHG context:	403520
Total unmethylated C's in CHH context:	1387911
Total unmethylated C's in Unknown context:	383

C methylated in CpG context:	27.1%
C methylated in CHG context:	1.9%
C methylated in CHH context:	8.5%
C methylated in Unknown context (CN or CHN):	9.2%


Bismark completed in 0d 2h 10m 41s