Bismark report for: zr2096_2_s1_R1_val_1.fq.gz and zr2096_2_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:	1000000
Number of paired-end alignments with a unique best hit:	503477
Mapping efficiency:	50.3% 
Sequence pairs with no alignments under any condition:	285525
Sequence pairs did not map uniquely:	210998
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:	126715	((converted) top strand)
GA/CT/CT:	124810	(complementary to (converted) top strand)
GA/CT/GA:	125599	(complementary to (converted) bottom strand)
CT/GA/GA:	126352	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	12425132

Total methylated C's in CpG context:	1171780
Total methylated C's in CHG context:	75002
Total methylated C's in CHH context:	557179
Total methylated C's in Unknown context:	51768


Total unmethylated C's in CpG context:	462498
Total unmethylated C's in CHG context:	2635229
Total unmethylated C's in CHH context:	7523444
Total unmethylated C's in Unknown context:	169378


C methylated in CpG context:	71.7%
C methylated in CHG context:	2.8%
C methylated in CHH context:	6.9%
C methylated in unknown context (CN or CHN):	23.4%


Bismark completed in 0d 0h 9m 48s