Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/4_TGACCA_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:	11408856
Number of alignments with a unique best hit from the different alignments:	4536160
Mapping efficiency:	39.8%
Sequences with no alignments under any condition:	1477731
Sequences did not map uniquely:	5394965
Sequences which were discarded because genomic sequence could not be extracted:	8697

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2075415	((converted) top strand)
CT/GA:	2075298	((converted) bottom strand)
GA/CT:	187772	(complementary to (converted) top strand)
GA/GA:	188978	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	25520936

Total methylated C's in CpG context:	1016597
Total methylated C's in CHG context:	68499
Total methylated C's in CHH context:	1376350
Total methylated C's in Unknown context:	409

Total unmethylated C's in CpG context:	2445956
Total unmethylated C's in CHG context:	4625068
Total unmethylated C's in CHH context:	15988466
Total unmethylated C's in Unknown context:	4191

C methylated in CpG context:	29.4%
C methylated in CHG context:	1.5%
C methylated in CHH context:	7.9%
C methylated in Unknown context (CN or CHN):	8.9%


Bismark completed in 0d 14h 30m 22s