Bismark report for: /Volumes/Serine/wd/18-04-10/sub-zr2096_5_s1_R1.fastq and /Volumes/Serine/wd/18-04-10/sub-zr2096_5_s1_R2.fastq (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:	10000
Number of paired-end alignments with a unique best hit:	4325
Mapping efficiency:	43.2% 
Sequence pairs with no alignments under any condition:	4278
Sequence pairs did not map uniquely:	1397
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:	1109	((converted) top strand)
GA/CT/CT:	1062	(complementary to (converted) top strand)
GA/CT/GA:	999	(complementary to (converted) bottom strand)
CT/GA/GA:	1155	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	147077

Total methylated C's in CpG context:	13317
Total methylated C's in CHG context:	1034
Total methylated C's in CHH context:	3173
Total methylated C's in Unknown context:	338


Total unmethylated C's in CpG context:	5822
Total unmethylated C's in CHG context:	32564
Total unmethylated C's in CHH context:	91167
Total unmethylated C's in Unknown context:	1203


C methylated in CpG context:	69.6%
C methylated in CHG context:	3.1%
C methylated in CHH context:	3.4%
C methylated in unknown context (CN or CHN):	21.9%


Bismark completed in 0d 0h 0m 21s