Bismark report for: /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R1.fastq.gz and /Volumes/Serine/wd/18-04-07/zr2096_6_s1_R2.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,-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:	1000
Number of paired-end alignments with a unique best hit:	517
Mapping efficiency:	51.7% 
Sequence pairs with no alignments under any condition:	302
Sequence pairs did not map uniquely:	181
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:	149	((converted) top strand)
GA/CT/CT:	107	(complementary to (converted) top strand)
GA/CT/GA:	136	(complementary to (converted) bottom strand)
CT/GA/GA:	125	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	16770

Total methylated C's in CpG context:	1717
Total methylated C's in CHG context:	112
Total methylated C's in CHH context:	449
Total methylated C's in Unknown context:	56


Total unmethylated C's in CpG context:	588
Total unmethylated C's in CHG context:	3620
Total unmethylated C's in CHH context:	10284
Total unmethylated C's in Unknown context:	239


C methylated in CpG context:	74.5%
C methylated in CHG context:	3.0%
C methylated in CHH context:	4.2%
C methylated in unknown context (CN or CHN):	19.0%


Bismark completed in 0d 0h 0m 15s