Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/8_ACTTGA_L001_R1_001_trimmed.fq.gz (version: v0.19.0)
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 /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/20180503_oly_genome_pbjelly_sjw_01_bismark/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	14269815
Number of alignments with a unique best hit from the different alignments:	7450760
Mapping efficiency:	52.2%
Sequences with no alignments under any condition:	1807284
Sequences did not map uniquely:	5011771
Sequences which were discarded because genomic sequence could not be extracted:	19179

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3567172	((converted) top strand)
CT/GA:	3566713	((converted) bottom strand)
GA/CT:	149624	(complementary to (converted) top strand)
GA/GA:	148072	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	57476895

Total methylated C's in CpG context:	2072002
Total methylated C's in CHG context:	165895
Total methylated C's in CHH context:	1839579
Total methylated C's in Unknown context:	31780

Total unmethylated C's in CpG context:	6356294
Total unmethylated C's in CHG context:	11147692
Total unmethylated C's in CHH context:	35895433
Total unmethylated C's in Unknown context:	174320

C methylated in CpG context:	24.6%
C methylated in CHG context:	1.5%
C methylated in CHH context:	4.9%
C methylated in Unknown context (CN or CHN):	15.4%


Bismark completed in 0d 15h 31m 22s