Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_17_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_17_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:	57429743
Number of paired-end alignments with a unique best hit:	35252677
Mapping efficiency:	61.4% 
Sequence pairs with no alignments under any condition:	12521081
Sequence pairs did not map uniquely:	9655985
Sequence pairs which were discarded because genomic sequence could not be extracted:	164

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8773352	((converted) top strand)
GA/CT/CT:	8819837	(complementary to (converted) top strand)
GA/CT/GA:	8852263	(complementary to (converted) bottom strand)
CT/GA/GA:	8807061	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1257976076

Total methylated C's in CpG context:	16913211
Total methylated C's in CHG context:	1080223
Total methylated C's in CHH context:	4465430
Total methylated C's in Unknown context:	41529

Total unmethylated C's in CpG context:	150059765
Total unmethylated C's in CHG context:	220480977
Total unmethylated C's in CHH context:	864976470
Total unmethylated C's in Unknown context:	2971793

C methylated in CpG context:	10.1%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.4%


Bismark completed in 0d 5h 33m 39s