Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/6_GCCAAT_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:	12409649
Number of alignments with a unique best hit from the different alignments:	5269110
Mapping efficiency:	42.5%
Sequences with no alignments under any condition:	3275362
Sequences did not map uniquely:	3865177
Sequences which were discarded because genomic sequence could not be extracted:	10014

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2577697	((converted) top strand)
CT/GA:	2575616	((converted) bottom strand)
GA/CT:	55210	(complementary to (converted) top strand)
GA/GA:	50573	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	40940100

Total methylated C's in CpG context:	1640749
Total methylated C's in CHG context:	127541
Total methylated C's in CHH context:	942648
Total methylated C's in Unknown context:	1916

Total unmethylated C's in CpG context:	4498550
Total unmethylated C's in CHG context:	8020739
Total unmethylated C's in CHH context:	25709873
Total unmethylated C's in Unknown context:	34838

C methylated in CpG context:	26.7%
C methylated in CHG context:	1.6%
C methylated in CHH context:	3.5%
C methylated in Unknown context (CN or CHN):	5.2%


Bismark completed in 0d 9h 24m 9s