Bismark report for: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_6_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_6_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:	191560039
Number of paired-end alignments with a unique best hit:	119684660
Mapping efficiency:	62.5% 
Sequence pairs with no alignments under any condition:	41837372
Sequence pairs did not map uniquely:	30038007
Sequence pairs which were discarded because genomic sequence could not be extracted:	12058

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	29988260	((converted) top strand)
GA/CT/CT:	29768713	(complementary to (converted) top strand)
GA/CT/GA:	29852231	(complementary to (converted) bottom strand)
CT/GA/GA:	30063398	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3820668638

Total methylated C's in CpG context:	56568946
Total methylated C's in CHG context:	3598036
Total methylated C's in CHH context:	15351455
Total methylated C's in Unknown context:	160518

Total unmethylated C's in CpG context:	454902768
Total unmethylated C's in CHG context:	690584257
Total unmethylated C's in CHH context:	2599663176
Total unmethylated C's in Unknown context:	9120689

C methylated in CpG context:	11.1%
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 53m 43s