Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_11_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_11_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-genome/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:	56063348
Number of paired-end alignments with a unique best hit:	34270614
Mapping efficiency:	61.1% 
Sequence pairs with no alignments under any condition:	14832830
Sequence pairs did not map uniquely:	6959904
Sequence pairs which were discarded because genomic sequence could not be extracted:	4580

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8553748	((converted) top strand)
GA/CT/CT:	8577936	(complementary to (converted) top strand)
GA/CT/GA:	8574939	(complementary to (converted) bottom strand)
CT/GA/GA:	8559411	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1206892002

Total methylated C's in CpG context:	16575220
Total methylated C's in CHG context:	1026274
Total methylated C's in CHH context:	4320799
Total methylated C's in Unknown context:	42248

Total unmethylated C's in CpG context:	137880004
Total unmethylated C's in CHG context:	210169564
Total unmethylated C's in CHH context:	836920141
Total unmethylated C's in Unknown context:	3005737

C methylated in CpG context:	10.7%
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 31m 17s