Bismark report for: /home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_5_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:	47401736
Number of alignments with a unique best hit from the different alignments:	16402431
Mapping efficiency:	34.6%
Sequences with no alignments under any condition:	12742540
Sequences did not map uniquely:	18256765
Sequences which were discarded because genomic sequence could not be extracted:	30092

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3709999	((converted) top strand)
CT/GA:	3688046	((converted) bottom strand)
GA/CT:	4511078	(complementary to (converted) top strand)
GA/GA:	4463216	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	96614715

Total methylated C's in CpG context:	10467052
Total methylated C's in CHG context:	400612
Total methylated C's in CHH context:	5387299
Total methylated C's in Unknown context:	2284

Total unmethylated C's in CpG context:	3184135
Total unmethylated C's in CHG context:	19480472
Total unmethylated C's in CHH context:	57695145
Total unmethylated C's in Unknown context:	16555

C methylated in CpG context:	76.7%
C methylated in CHG context:	2.0%
C methylated in CHH context:	8.5%
C methylated in Unknown context (CN or CHN):	12.1%


Bismark completed in 11d 2h 44m 35s