Bismark report for: /Volumes/Serine/wd/18-04-07/zr2096_8_s1_R1.fastq.gz and /Volumes/Serine/wd/18-04-07/zr2096_8_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:	29761837
Number of paired-end alignments with a unique best hit:	4646143
Mapping efficiency:	15.6% 
Sequence pairs with no alignments under any condition:	23487537
Sequence pairs did not map uniquely:	1628157
Sequence pairs which were discarded because genomic sequence could not be extracted:	2

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2325979	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	2320162	((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:	157822868

Total methylated C's in CpG context:	14123725
Total methylated C's in CHG context:	1232277
Total methylated C's in CHH context:	5100411
Total methylated C's in Unknown context:	204421


Total unmethylated C's in CpG context:	5895006
Total unmethylated C's in CHG context:	35229169
Total unmethylated C's in CHH context:	96242280
Total unmethylated C's in Unknown context:	663867


C methylated in CpG context:	70.6%
C methylated in CHG context:	3.4%
C methylated in CHH context:	5.0%
C methylated in unknown context (CN or CHN):	23.5%


Bismark completed in 0d 1h 58m 10s