Bismark report for: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_2_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_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/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:	164737166
Number of paired-end alignments with a unique best hit:	103087584
Mapping efficiency:	62.6% 
Sequence pairs with no alignments under any condition:	37247825
Sequence pairs did not map uniquely:	24401757
Sequence pairs which were discarded because genomic sequence could not be extracted:	11462

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	25819132	((converted) top strand)
GA/CT/CT:	25684248	(complementary to (converted) top strand)
GA/CT/GA:	25715010	(complementary to (converted) bottom strand)
CT/GA/GA:	25857732	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3444022931

Total methylated C's in CpG context:	50751840
Total methylated C's in CHG context:	3314562
Total methylated C's in CHH context:	13873691
Total methylated C's in Unknown context:	137554

Total unmethylated C's in CpG context:	412119007
Total unmethylated C's in CHG context:	621569062
Total unmethylated C's in CHH context:	2342394769
Total unmethylated C's in Unknown context:	8332795

C methylated in CpG context:	11.0%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	1.6%


Bismark completed in 0d 15h 50m 47s