Bismark report for: /gscratch/srlab/sr320/data/cg/zr3534_4_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_4_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/ 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:	74728031
Number of paired-end alignments with a unique best hit:	45883964
Mapping efficiency:	61.4% 
Sequence pairs with no alignments under any condition:	16796021
Sequence pairs did not map uniquely:	12048046
Sequence pairs which were discarded because genomic sequence could not be extracted:	75

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	11411940	((converted) top strand)
GA/CT/CT:	11492615	(complementary to (converted) top strand)
GA/CT/GA:	11530375	(complementary to (converted) bottom strand)
CT/GA/GA:	11448959	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1598583776

Total methylated C's in CpG context:	23340365
Total methylated C's in CHG context:	1383619
Total methylated C's in CHH context:	5876339
Total methylated C's in Unknown context:	57437

Total unmethylated C's in CpG context:	184727627
Total unmethylated C's in CHG context:	278325475
Total unmethylated C's in CHH context:	1104930351
Total unmethylated C's in Unknown context:	3918703

C methylated in CpG context:	11.2%
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 6h 33m 29s