Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/5_ACAGTG_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:	12502181
Number of alignments with a unique best hit from the different alignments:	6565485
Mapping efficiency:	52.5%
Sequences with no alignments under any condition:	1566378
Sequences did not map uniquely:	4370318
Sequences which were discarded because genomic sequence could not be extracted:	16973

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3136437	((converted) top strand)
CT/GA:	3144162	((converted) bottom strand)
GA/CT:	131919	(complementary to (converted) top strand)
GA/GA:	135994	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	50755672

Total methylated C's in CpG context:	1984755
Total methylated C's in CHG context:	149001
Total methylated C's in CHH context:	1826039
Total methylated C's in Unknown context:	28729

Total unmethylated C's in CpG context:	5498703
Total unmethylated C's in CHG context:	9800659
Total unmethylated C's in CHH context:	31496515
Total unmethylated C's in Unknown context:	160224

C methylated in CpG context:	26.5%
C methylated in CHG context:	1.5%
C methylated in CHH context:	5.5%
C methylated in Unknown context (CN or CHN):	15.2%


Bismark completed in 0d 9h 26m 51s