Bismark report for: /gscratch/srlab/sr320/data/cg/zr3534_9_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_9_R2.fastp-trim.20201202.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 8 --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:	73776588
Number of paired-end alignments with a unique best hit:	45591578
Mapping efficiency:	61.8% 
Sequence pairs with no alignments under any condition:	16002262
Sequence pairs did not map uniquely:	12182748
Sequence pairs which were discarded because genomic sequence could not be extracted:	120

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	11364394	((converted) top strand)
GA/CT/CT:	11385517	(complementary to (converted) top strand)
GA/CT/GA:	11430000	(complementary to (converted) bottom strand)
CT/GA/GA:	11411547	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1595529090

Total methylated C's in CpG context:	21006842
Total methylated C's in CHG context:	1277934
Total methylated C's in CHH context:	5350483
Total methylated C's in Unknown context:	49317

Total unmethylated C's in CpG context:	188873033
Total unmethylated C's in CHG context:	281019136
Total unmethylated C's in CHH context:	1098001662
Total unmethylated C's in Unknown context:	3841672

C methylated in CpG context:	10.0%
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 15h 22m 20s