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/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:	403617
Mapping efficiency:	40.4%
Sequences with no alignments under any condition:	118458
Sequences did not map uniquely:	477925
Sequences which were discarded because genomic sequence could not be extracted:	739

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	186159	((converted) top strand)
CT/GA:	185612	((converted) bottom strand)
GA/CT:	15553	(complementary to (converted) top strand)
GA/GA:	15554	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2264438

Total methylated C's in CpG context:	89788
Total methylated C's in CHG context:	5604
Total methylated C's in CHH context:	114714
Total methylated C's in Unknown context:	34

Total unmethylated C's in CpG context:	217439
Total unmethylated C's in CHG context:	412460
Total unmethylated C's in CHH context:	1424433
Total unmethylated C's in Unknown context:	356

C methylated in CpG context:	29.2%
C methylated in CHG context:	1.3%
C methylated in CHH context:	7.5%
C methylated in Unknown context (CN or CHN):	8.7%


Bismark completed in 0d 1h 27m 41s