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,-0.6 -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:	58102004
Number of paired-end alignments with a unique best hit:	36100179
Mapping efficiency:	62.1% 
Sequence pairs with no alignments under any condition:	14852748
Sequence pairs did not map uniquely:	7149077
Sequence pairs which were discarded because genomic sequence could not be extracted:	4297

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	9028133	((converted) top strand)
GA/CT/CT:	9015692	(complementary to (converted) top strand)
GA/CT/GA:	9020563	(complementary to (converted) bottom strand)
CT/GA/GA:	9031494	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1270966403

Total methylated C's in CpG context:	18346891
Total methylated C's in CHG context:	1100305
Total methylated C's in CHH context:	4731062
Total methylated C's in Unknown context:	44588

Total unmethylated C's in CpG context:	142823649
Total unmethylated C's in CHG context:	219609453
Total unmethylated C's in CHH context:	884355043
Total unmethylated C's in Unknown context:	3189323

C methylated in CpG context:	11.4%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.4%


Bismark completed in 0d 5h 39m 32s