Bismark report for: ../../data/Haws-10/zr3644_6_R1_val_1_val_1_val_1.fq.gz and ../../data/Haws-10/zr3644_6_R2_val_2_val_2_val_2.fq.gz (version: v0.24.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /home/shared/16TB_HDD_01/sr320/github/project-oyster-oa/data/Haws-10/ with the specified options: -q --score-min L,0,-0.8 -p 8 --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:	53174813
Number of paired-end alignments with a unique best hit:	33775198
Mapping efficiency:	63.5% 
Sequence pairs with no alignments under any condition:	10766456
Sequence pairs did not map uniquely:	8633159
Sequence pairs which were discarded because genomic sequence could not be extracted:	12

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8437241	((converted) top strand)
GA/CT/CT:	8432031	(complementary to (converted) top strand)
GA/CT/GA:	8450279	(complementary to (converted) bottom strand)
CT/GA/GA:	8455635	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1186147678

Total methylated C's in CpG context:	15630526
Total methylated C's in CHG context:	1018157
Total methylated C's in CHH context:	4534792
Total methylated C's in Unknown context:	64717

Total unmethylated C's in CpG context:	133867658
Total unmethylated C's in CHG context:	203425401
Total unmethylated C's in CHH context:	827671144
Total unmethylated C's in Unknown context:	3915474

C methylated in CpG context:	10.5%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.6%


Bismark completed in 0d 4h 44m 56s