Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/2_CGATGT_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/srlab/sam/data/O_lurida/oly_genome_assemblies/Olurida_v081/oly_v081_bismark_genome/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	11879398
Number of alignments with a unique best hit from the different alignments:	6010969
Mapping efficiency:	50.6%
Sequences with no alignments under any condition:	1790583
Sequences did not map uniquely:	4077846
Sequences which were discarded because genomic sequence could not be extracted:	4344

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2853263	((converted) top strand)
CT/GA:	2858218	((converted) bottom strand)
GA/CT:	147382	(complementary to (converted) top strand)
GA/GA:	147762	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	46571499

Total methylated C's in CpG context:	1799874
Total methylated C's in CHG context:	196436
Total methylated C's in CHH context:	1854737
Total methylated C's in Unknown context:	29004

Total unmethylated C's in CpG context:	4959661
Total unmethylated C's in CHG context:	8836010
Total unmethylated C's in CHH context:	28924781
Total unmethylated C's in Unknown context:	156484

C methylated in CpG context:	26.6%
C methylated in CHG context:	2.2%
C methylated in CHH context:	6.0%
C methylated in Unknown context (CN or CHN):	15.6%


Bismark completed in 0d 3h 22m 13s