Bismark report for: /Volumes/Serine/wd/18-04-27/zr2096_3_s1_R1_val_1.fq.gz and /Volumes/Serine/wd/18-04-27/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,-0.9 -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:	29548753
Number of paired-end alignments with a unique best hit:	13093747
Mapping efficiency:	44.3% 
Sequence pairs with no alignments under any condition:	10404990
Sequence pairs did not map uniquely:	6050016
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:	3279278	((converted) top strand)
GA/CT/CT:	3253127	(complementary to (converted) top strand)
GA/CT/GA:	3268922	(complementary to (converted) bottom strand)
CT/GA/GA:	3292419	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	364333091

Total methylated C's in CpG context:	42231693
Total methylated C's in CHG context:	1748101
Total methylated C's in CHH context:	6570371
Total methylated C's in Unknown context:	473894


Total unmethylated C's in CpG context:	11323986
Total unmethylated C's in CHG context:	81087161
Total unmethylated C's in CHH context:	221371779
Total unmethylated C's in Unknown context:	2480520


C methylated in CpG context:	78.9%
C methylated in CHG context:	2.1%
C methylated in CHH context:	2.9%
C methylated in unknown context (CN or CHN):	16.0%


Bismark completed in 0d 4h 29m 43s