Bismark report for: /Volumes/Serine/wd/18-03-16/10_32_S32_L001_R1_001.fastq.gz and /Volumes/Serine/wd/18-03-16/10_32_S32_L001_R2_001.fastq.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,-0.6 --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:	574346
Number of paired-end alignments with a unique best hit:	230846
Mapping efficiency:	40.2% 
Sequence pairs with no alignments under any condition:	262321
Sequence pairs did not map uniquely:	81179
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:	37825	((converted) top strand)
GA/CT/CT:	77060	(complementary to (converted) top strand)
GA/CT/GA:	78343	(complementary to (converted) bottom strand)
CT/GA/GA:	37618	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	6729925

Total methylated C's in CpG context:	689306
Total methylated C's in CHG context:	15135
Total methylated C's in CHH context:	47064
Total methylated C's in Unknown context:	2799


Total unmethylated C's in CpG context:	258687
Total unmethylated C's in CHG context:	1469826
Total unmethylated C's in CHH context:	4249907
Total unmethylated C's in Unknown context:	19823


C methylated in CpG context:	72.7%
C methylated in CHG context:	1.0%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	12.4%


Bismark completed in 0d 0h 4m 43s