Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_3_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_3_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:	38671370
Number of paired-end alignments with a unique best hit:	14495047
Mapping efficiency:	37.5% 
Sequence pairs with no alignments under any condition:	20552780
Sequence pairs did not map uniquely:	3623543
Sequence pairs which were discarded because genomic sequence could not be extracted:	662

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3626646	((converted) top strand)
GA/CT/CT:	3609892	(complementary to (converted) top strand)
GA/CT/GA:	3623071	(complementary to (converted) bottom strand)
CT/GA/GA:	3634776	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	516148236

Total methylated C's in CpG context:	7919903
Total methylated C's in CHG context:	395449
Total methylated C's in CHH context:	1573639
Total methylated C's in Unknown context:	3552

Total unmethylated C's in CpG context:	58489919
Total unmethylated C's in CHG context:	90789163
Total unmethylated C's in CHH context:	356980163
Total unmethylated C's in Unknown context:	356073

C methylated in CpG context:	11.9%
C methylated in CHG context:	0.4%
C methylated in CHH context:	0.4%
C methylated in unknown context (CN or CHN):	1.0%


Bismark completed in 0d 5h 3m 14s