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 '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	31778715
Number of paired-end alignments with a unique best hit:	5499890
Mapping efficiency:	17.3% 
Sequence pairs with no alignments under any condition:	24300069
Sequence pairs did not map uniquely:	1978756
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2749961	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	2749928	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	189151053

Total methylated C's in CpG context:	17864954
Total methylated C's in CHG context:	1429272
Total methylated C's in CHH context:	5654793
Total methylated C's in Unknown context:	253526


Total unmethylated C's in CpG context:	7027555
Total unmethylated C's in CHG context:	41425253
Total unmethylated C's in CHH context:	115749226
Total unmethylated C's in Unknown context:	809323


C methylated in CpG context:	71.8%
C methylated in CHG context:	3.3%
C methylated in CHH context:	4.7%
C methylated in unknown context (CN or CHN):	23.9%


Bismark completed in 0d 2h 14m 53s