Bismark report for: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_3_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_3_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/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ 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:	184625873
Number of paired-end alignments with a unique best hit:	115959769
Mapping efficiency:	62.8% 
Sequence pairs with no alignments under any condition:	40261338
Sequence pairs did not map uniquely:	28404766
Sequence pairs which were discarded because genomic sequence could not be extracted:	11248

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	29066834	((converted) top strand)
GA/CT/CT:	28943533	(complementary to (converted) top strand)
GA/CT/GA:	28910221	(complementary to (converted) bottom strand)
CT/GA/GA:	29027933	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3698776401

Total methylated C's in CpG context:	55232294
Total methylated C's in CHG context:	3406696
Total methylated C's in CHH context:	14523371
Total methylated C's in Unknown context:	153488

Total unmethylated C's in CpG context:	433812436
Total unmethylated C's in CHG context:	664656714
Total unmethylated C's in CHH context:	2527144890
Total unmethylated C's in Unknown context:	8861712

C methylated in CpG context:	11.3%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	1.7%


Bismark completed in 0d 17h 28m 22s