Bismark report for: zr2096_3_s1_R1_val_1.fq.gz and zr2096_3_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:	526410
Mapping efficiency:	52.6% 
Sequence pairs with no alignments under any condition:	249675
Sequence pairs did not map uniquely:	223915
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:	131363	((converted) top strand)
GA/CT/CT:	131574	(complementary to (converted) top strand)
GA/CT/GA:	131909	(complementary to (converted) bottom strand)
CT/GA/GA:	131563	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	14440042

Total methylated C's in CpG context:	1612313
Total methylated C's in CHG context:	77322
Total methylated C's in CHH context:	361714
Total methylated C's in Unknown context:	36630


Total unmethylated C's in CpG context:	469203
Total unmethylated C's in CHG context:	3140194
Total unmethylated C's in CHH context:	8779296
Total unmethylated C's in Unknown context:	172384


C methylated in CpG context:	77.5%
C methylated in CHG context:	2.4%
C methylated in CHH context:	4.0%
C methylated in unknown context (CN or CHN):	17.5%


Bismark completed in 0d 0h 10m 19s