Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_14_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_14_R2.fastp-trim.20201206.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,-0.2 -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:	36184563
Number of paired-end alignments with a unique best hit:	13543064
Mapping efficiency:	37.4% 
Sequence pairs with no alignments under any condition:	19378814
Sequence pairs did not map uniquely:	3262685
Sequence pairs which were discarded because genomic sequence could not be extracted:	540

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3381915	((converted) top strand)
GA/CT/CT:	3386033	(complementary to (converted) top strand)
GA/CT/GA:	3387373	(complementary to (converted) bottom strand)
CT/GA/GA:	3387203	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	480027296

Total methylated C's in CpG context:	8480484
Total methylated C's in CHG context:	392938
Total methylated C's in CHH context:	1533847
Total methylated C's in Unknown context:	3945

Total unmethylated C's in CpG context:	53333962
Total unmethylated C's in CHG context:	84692824
Total unmethylated C's in CHH context:	331593241
Total unmethylated C's in Unknown context:	320465

C methylated in CpG context:	13.7%
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 1h 45m 16s