Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/4_TGACCA_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,-0.2 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	11560658
Number of alignments with a unique best hit from the different alignments:	5038185
Mapping efficiency:	43.6%
Sequences with no alignments under any condition:	2902106
Sequences did not map uniquely:	3620367
Sequences which were discarded because genomic sequence could not be extracted:	9284

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2483585	((converted) top strand)
CT/GA:	2478522	((converted) bottom strand)
GA/CT:	33228	(complementary to (converted) top strand)
GA/GA:	33566	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	39013786

Total methylated C's in CpG context:	1647867
Total methylated C's in CHG context:	75737
Total methylated C's in CHH context:	679888
Total methylated C's in Unknown context:	1531

Total unmethylated C's in CpG context:	4125544
Total unmethylated C's in CHG context:	7644415
Total unmethylated C's in CHH context:	24840335
Total unmethylated C's in Unknown context:	32365

C methylated in CpG context:	28.5%
C methylated in CHG context:	1.0%
C methylated in CHH context:	2.7%
C methylated in Unknown context (CN or CHN):	4.5%


Bismark completed in 0d 6h 3m 9s