Bismark report for: /gscratch/srlab/sr320/data/cg/zr3534_9_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_9_R2.fastp-trim.20201202.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-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:	73776588
Number of paired-end alignments with a unique best hit:	46249576
Mapping efficiency:	62.7% 
Sequence pairs with no alignments under any condition:	18427528
Sequence pairs did not map uniquely:	9099484
Sequence pairs which were discarded because genomic sequence could not be extracted:	5273

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	11561829	((converted) top strand)
GA/CT/CT:	11578586	(complementary to (converted) top strand)
GA/CT/GA:	11565150	(complementary to (converted) bottom strand)
CT/GA/GA:	11538738	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1614930893

Total methylated C's in CpG context:	21402276
Total methylated C's in CHG context:	1304086
Total methylated C's in CHH context:	5550413
Total methylated C's in Unknown context:	49721

Total unmethylated C's in CpG context:	188596358
Total unmethylated C's in CHG context:	285271601
Total unmethylated C's in CHH context:	1112806159
Total unmethylated C's in Unknown context:	3962829

C methylated in CpG context:	10.2%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.2%


Bismark completed in 0d 7h 12m 49s