Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_2_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_2_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:	55025914
Number of paired-end alignments with a unique best hit:	33388393
Mapping efficiency:	60.7% 
Sequence pairs with no alignments under any condition:	12972059
Sequence pairs did not map uniquely:	8665462
Sequence pairs which were discarded because genomic sequence could not be extracted:	120

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8328453	((converted) top strand)
GA/CT/CT:	8319972	(complementary to (converted) top strand)
GA/CT/GA:	8363956	(complementary to (converted) bottom strand)
CT/GA/GA:	8375892	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1195501862

Total methylated C's in CpG context:	15540506
Total methylated C's in CHG context:	983606
Total methylated C's in CHH context:	4120629
Total methylated C's in Unknown context:	38661

Total unmethylated C's in CpG context:	139270636
Total unmethylated C's in CHG context:	205694628
Total unmethylated C's in CHH context:	829891857
Total unmethylated C's in Unknown context:	2941456

C methylated in CpG context:	10.0%
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 5h 21m 24s