Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_22_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_22_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:	47019646
Number of paired-end alignments with a unique best hit:	29164293
Mapping efficiency:	62.0% 
Sequence pairs with no alignments under any condition:	12055540
Sequence pairs did not map uniquely:	5799813
Sequence pairs which were discarded because genomic sequence could not be extracted:	3674

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7261504	((converted) top strand)
GA/CT/CT:	7309226	(complementary to (converted) top strand)
GA/CT/GA:	7317228	(complementary to (converted) bottom strand)
CT/GA/GA:	7272661	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1035254685

Total methylated C's in CpG context:	14078388
Total methylated C's in CHG context:	898075
Total methylated C's in CHH context:	3733158
Total methylated C's in Unknown context:	33672

Total unmethylated C's in CpG context:	118463031
Total unmethylated C's in CHG context:	181180018
Total unmethylated C's in CHH context:	716902015
Total unmethylated C's in Unknown context:	2536356

C methylated in CpG context:	10.6%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.3%


Bismark completed in 0d 4h 37m 6s