Bismark report for: /Volumes/Serine/wd/18-04-10/trim14/zr2096_6_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-10/trim14/zr2096_6_s1_R2_val_2.fq.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,-1.2 -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:	24080119
Number of paired-end alignments with a unique best hit:	13889795
Mapping efficiency:	57.7% 
Sequence pairs with no alignments under any condition:	5415629
Sequence pairs did not map uniquely:	4774695
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3653608	((converted) top strand)
GA/CT/CT:	3286595	(complementary to (converted) top strand)
GA/CT/GA:	3290365	(complementary to (converted) bottom strand)
CT/GA/GA:	3659227	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	380247018

Total methylated C's in CpG context:	36675468
Total methylated C's in CHG context:	2049817
Total methylated C's in CHH context:	9632476
Total methylated C's in Unknown context:	1019260


Total unmethylated C's in CpG context:	13557194
Total unmethylated C's in CHG context:	81881435
Total unmethylated C's in CHH context:	236450628
Total unmethylated C's in Unknown context:	5065365


C methylated in CpG context:	73.0%
C methylated in CHG context:	2.4%
C methylated in CHH context:	3.9%
C methylated in unknown context (CN or CHN):	16.8%


Bismark completed in 0d 4h 19m 45s