Bismark report for: /gscratch/srlab/sr320/data/cg/zr3644_16_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_16_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:	50134077
Number of paired-end alignments with a unique best hit:	31344702
Mapping efficiency:	62.5% 
Sequence pairs with no alignments under any condition:	12085635
Sequence pairs did not map uniquely:	6703740
Sequence pairs which were discarded because genomic sequence could not be extracted:	3712

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7821783	((converted) top strand)
GA/CT/CT:	7841389	(complementary to (converted) top strand)
GA/CT/GA:	7849611	(complementary to (converted) bottom strand)
CT/GA/GA:	7828207	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1088871217

Total methylated C's in CpG context:	14928270
Total methylated C's in CHG context:	917631
Total methylated C's in CHH context:	3921327
Total methylated C's in Unknown context:	36292

Total unmethylated C's in CpG context:	123938584
Total unmethylated C's in CHG context:	189497153
Total unmethylated C's in CHH context:	755668252
Total unmethylated C's in Unknown context:	2681441

C methylated in CpG context:	10.8%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.3%


Bismark completed in 0d 4h 51m 48s