Bismark report for: /Volumes/Serine/wd/18-04-07/zr2096_9_s1_R1.fastq.gz and /Volumes/Serine/wd/18-04-07/zr2096_9_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:	32636231
Number of paired-end alignments with a unique best hit:	5644532
Mapping efficiency:	17.3% 
Sequence pairs with no alignments under any condition:	24857593
Sequence pairs did not map uniquely:	2134106
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:	2816231	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	2828300	((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:	203684656

Total methylated C's in CpG context:	23798172
Total methylated C's in CHG context:	1639976
Total methylated C's in CHH context:	5453380
Total methylated C's in Unknown context:	272146


Total unmethylated C's in CpG context:	6006825
Total unmethylated C's in CHG context:	45798164
Total unmethylated C's in CHH context:	120988139
Total unmethylated C's in Unknown context:	826171


C methylated in CpG context:	79.8%
C methylated in CHG context:	3.5%
C methylated in CHH context:	4.3%
C methylated in unknown context (CN or CHN):	24.8%


Bismark completed in 0d 2h 19m 33s