Bismark report for: zr2096_4_s1_R1_val_1.fq.gz and zr2096_4_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:	541137
Mapping efficiency:	54.1% 
Sequence pairs with no alignments under any condition:	234921
Sequence pairs did not map uniquely:	223942
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:	137788	((converted) top strand)
GA/CT/CT:	132258	(complementary to (converted) top strand)
GA/CT/GA:	133147	(complementary to (converted) bottom strand)
CT/GA/GA:	137944	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	13656928

Total methylated C's in CpG context:	1167119
Total methylated C's in CHG context:	68888
Total methylated C's in CHH context:	408851
Total methylated C's in Unknown context:	37082


Total unmethylated C's in CpG context:	579377
Total unmethylated C's in CHG context:	2907466
Total unmethylated C's in CHH context:	8525227
Total unmethylated C's in Unknown context:	172449


C methylated in CpG context:	66.8%
C methylated in CHG context:	2.3%
C methylated in CHH context:	4.6%
C methylated in unknown context (CN or CHN):	17.7%


Bismark completed in 0d 0h 10m 4s