Bismark report for: /gscratch/scrubbed/samwhite/data/O_lurida/BSseq/whole_genome_BSseq_reads/20180830_trimgalore/1_ATCACG_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:	9365330
Number of alignments with a unique best hit from the different alignments:	4066105
Mapping efficiency:	43.4%
Sequences with no alignments under any condition:	2378548
Sequences did not map uniquely:	2920677
Sequences which were discarded because genomic sequence could not be extracted:	7494

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2002168	((converted) top strand)
CT/GA:	1999822	((converted) bottom strand)
GA/CT:	27767	(complementary to (converted) top strand)
GA/GA:	28854	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	31606927

Total methylated C's in CpG context:	1332201
Total methylated C's in CHG context:	73999
Total methylated C's in CHH context:	573400
Total methylated C's in Unknown context:	1354

Total unmethylated C's in CpG context:	3374891
Total unmethylated C's in CHG context:	6217392
Total unmethylated C's in CHH context:	20035044
Total unmethylated C's in Unknown context:	27054

C methylated in CpG context:	28.3%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.8%
C methylated in Unknown context (CN or CHN):	4.8%


Bismark completed in 0d 1h 16m 30s