Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/7_CAGATC_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/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:	10113854
Number of alignments with a unique best hit from the different alignments:	3984767
Mapping efficiency:	39.4%
Sequences with no alignments under any condition:	1329633
Sequences did not map uniquely:	4799454
Sequences which were discarded because genomic sequence could not be extracted:	7873

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	1824319	((converted) top strand)
CT/GA:	1820642	((converted) bottom strand)
GA/CT:	165565	(complementary to (converted) top strand)
GA/GA:	166368	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	22414088

Total methylated C's in CpG context:	854767
Total methylated C's in CHG context:	57383
Total methylated C's in CHH context:	1200345
Total methylated C's in Unknown context:	349

Total unmethylated C's in CpG context:	2163006
Total unmethylated C's in CHG context:	4071784
Total unmethylated C's in CHH context:	14066803
Total unmethylated C's in Unknown context:	3847

C methylated in CpG context:	28.3%
C methylated in CHG context:	1.4%
C methylated in CHH context:	7.9%
C methylated in Unknown context (CN or CHN):	8.3%


Bismark completed in 1d 1h 51m 27s