Bismark report for: /Volumes/Serine/wd/18-04-10/10_10/sub-zr2096_5_s1_R1_val_1.fq and /Volumes/Serine/wd/18-04-10/10_10/sub-zr2096_5_s1_R2_val_2.fq (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:	9896
Number of paired-end alignments with a unique best hit:	5200
Mapping efficiency:	52.5% 
Sequence pairs with no alignments under any condition:	2773
Sequence pairs did not map uniquely:	1923
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:	1345	((converted) top strand)
GA/CT/CT:	1242	(complementary to (converted) top strand)
GA/CT/GA:	1224	(complementary to (converted) bottom strand)
CT/GA/GA:	1389	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	136571

Total methylated C's in CpG context:	11867
Total methylated C's in CHG context:	798
Total methylated C's in CHH context:	4637
Total methylated C's in Unknown context:	401


Total unmethylated C's in CpG context:	5344
Total unmethylated C's in CHG context:	28548
Total unmethylated C's in CHH context:	85377
Total unmethylated C's in Unknown context:	1605


C methylated in CpG context:	69.0%
C methylated in CHG context:	2.7%
C methylated in CHH context:	5.2%
C methylated in unknown context (CN or CHN):	20.0%


Bismark completed in 0d 0h 0m 21s