Bismark report for: /Volumes/Serine/wd/18-04-07/zr2096_5_s1_R1.fastq.gz and /Volumes/Serine/wd/18-04-07/zr2096_5_s1_R2.fastq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /Volumes/Serine/wd/18-03-15/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	31778715
Number of paired-end alignments with a unique best hit:	10617999
Mapping efficiency:	33.4% 
Sequence pairs with no alignments under any condition:	17366736
Sequence pairs did not map uniquely:	3793980
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2702790	((converted) top strand)
GA/CT/CT:	2609389	(complementary to (converted) top strand)
GA/CT/GA:	2601979	(complementary to (converted) bottom strand)
CT/GA/GA:	2703838	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	366537981

Total methylated C's in CpG context:	34486919
Total methylated C's in CHG context:	2210810
Total methylated C's in CHH context:	6230765
Total methylated C's in Unknown context:	438615


Total unmethylated C's in CpG context:	13926155
Total unmethylated C's in CHG context:	82047506
Total unmethylated C's in CHH context:	227635826
Total unmethylated C's in Unknown context:	1526433


C methylated in CpG context:	71.2%
C methylated in CHG context:	2.6%
C methylated in CHH context:	2.7%
C methylated in unknown context (CN or CHN):	22.3%


Bismark completed in 0d 4h 34m 27s