Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_1_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_1_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:	50613363
Number of paired-end alignments with a unique best hit:	31733639
Mapping efficiency:	62.7% 
Sequence pairs with no alignments under any condition:	12202916
Sequence pairs did not map uniquely:	6676808
Sequence pairs which were discarded because genomic sequence could not be extracted:	3659

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7979296	((converted) top strand)
GA/CT/CT:	7883292	(complementary to (converted) top strand)
GA/CT/GA:	7883674	(complementary to (converted) bottom strand)
CT/GA/GA:	7983718	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1112435555

Total methylated C's in CpG context:	13822220
Total methylated C's in CHG context:	906946
Total methylated C's in CHH context:	3907246
Total methylated C's in Unknown context:	33720

Total unmethylated C's in CpG context:	127230281
Total unmethylated C's in CHG context:	193885510
Total unmethylated C's in CHH context:	772683352
Total unmethylated C's in Unknown context:	2727121

C methylated in CpG context:	9.8%
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 4h 55m 53s