Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_1_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_1_R2_val_2_val_2_val_2.fq.gz (version: v0.22.3)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/yaaminiv/Hawes/data/Cg-roslin/ with the specified options: -q --score-min L,0,-0.6 -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:	50993451
Number of paired-end alignments with a unique best hit:	31434721
Mapping efficiency:	61.6% 
Sequence pairs with no alignments under any condition:	11134052
Sequence pairs did not map uniquely:	8424678
Sequence pairs which were discarded because genomic sequence could not be extracted:	115

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7891335	((converted) top strand)
GA/CT/CT:	7795639	(complementary to (converted) top strand)
GA/CT/GA:	7818927	(complementary to (converted) bottom strand)
CT/GA/GA:	7928705	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1113134972

Total methylated C's in CpG context:	13763919
Total methylated C's in CHG context:	897841
Total methylated C's in CHH context:	3720045
Total methylated C's in Unknown context:	35255

Total unmethylated C's in CpG context:	131347662
Total unmethylated C's in CHG context:	194126289
Total unmethylated C's in CHH context:	769279216
Total unmethylated C's in Unknown context:	2644308

C methylated in CpG context:	9.5%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.3%


Bismark completed in 0d 4h 56m 59s