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/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:	11879398
Number of alignments with a unique best hit from the different alignments:	6229488
Mapping efficiency:	52.4%
Sequences with no alignments under any condition:	1480776
Sequences did not map uniquely:	4169134
Sequences which were discarded because genomic sequence could not be extracted:	15981

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2964533	((converted) top strand)
CT/GA:	2969424	((converted) bottom strand)
GA/CT:	140820	(complementary to (converted) top strand)
GA/GA:	138730	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	48108016

Total methylated C's in CpG context:	1870637
Total methylated C's in CHG context:	202679
Total methylated C's in CHH context:	1823533
Total methylated C's in Unknown context:	26029

Total unmethylated C's in CpG context:	5123537
Total unmethylated C's in CHG context:	9169356
Total unmethylated C's in CHH context:	29918274
Total unmethylated C's in Unknown context:	143090

C methylated in CpG context:	26.7%
C methylated in CHG context:	2.2%
C methylated in CHH context:	5.7%
C methylated in Unknown context (CN or CHN):	15.4%


Bismark completed in 0d 3h 30m 32s