Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_4_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_4_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:	49072984
Number of paired-end alignments with a unique best hit:	18288301
Mapping efficiency:	37.3% 
Sequence pairs with no alignments under any condition:	26298409
Sequence pairs did not map uniquely:	4486274
Sequence pairs which were discarded because genomic sequence could not be extracted:	669

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4594086	((converted) top strand)
GA/CT/CT:	4547569	(complementary to (converted) top strand)
GA/CT/GA:	4551018	(complementary to (converted) bottom strand)
CT/GA/GA:	4594959	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	651332942

Total methylated C's in CpG context:	9707910
Total methylated C's in CHG context:	484408
Total methylated C's in CHH context:	1922996
Total methylated C's in Unknown context:	4291

Total unmethylated C's in CpG context:	73601851
Total unmethylated C's in CHG context:	113783118
Total unmethylated C's in CHH context:	451832659
Total unmethylated C's in Unknown context:	448038

C methylated in CpG context:	11.7%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.4%
C methylated in unknown context (CN or CHN):	0.9%


Bismark completed in 0d 2h 21m 52s