Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/7_CAGATC_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:	10253191
Number of alignments with a unique best hit from the different alignments:	5382140
Mapping efficiency:	52.5%
Sequences with no alignments under any condition:	1289656
Sequences did not map uniquely:	3581395
Sequences which were discarded because genomic sequence could not be extracted:	14015

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2588855	((converted) top strand)
CT/GA:	2588882	((converted) bottom strand)
GA/CT:	95465	(complementary to (converted) top strand)
GA/GA:	94923	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	41275205

Total methylated C's in CpG context:	1610454
Total methylated C's in CHG context:	98157
Total methylated C's in CHH context:	1236583
Total methylated C's in Unknown context:	21382

Total unmethylated C's in CpG context:	4341462
Total unmethylated C's in CHG context:	7971801
Total unmethylated C's in CHH context:	26016748
Total unmethylated C's in Unknown context:	121435

C methylated in CpG context:	27.1%
C methylated in CHG context:	1.2%
C methylated in CHH context:	4.5%
C methylated in Unknown context (CN or CHN):	15.0%


Bismark completed in 0d 13h 10m 16s