Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_15_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_15_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:	58102004
Number of paired-end alignments with a unique best hit:	22135736
Mapping efficiency:	38.1% 
Sequence pairs with no alignments under any condition:	30647323
Sequence pairs did not map uniquely:	5318945
Sequence pairs which were discarded because genomic sequence could not be extracted:	911

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	5563993	((converted) top strand)
GA/CT/CT:	5501241	(complementary to (converted) top strand)
GA/CT/GA:	5504319	(complementary to (converted) bottom strand)
CT/GA/GA:	5565272	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	787565112

Total methylated C's in CpG context:	13137960
Total methylated C's in CHG context:	629574
Total methylated C's in CHH context:	2500759
Total methylated C's in Unknown context:	6039

Total unmethylated C's in CpG context:	88228425
Total unmethylated C's in CHG context:	138512773
Total unmethylated C's in CHH context:	544555621
Total unmethylated C's in Unknown context:	545051

C methylated in CpG context:	13.0%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.1%


Bismark completed in 0d 2h 52m 13s