Bismark report for: /gscratch/srlab/sr320/data/cg/zr3534_1_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_1_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:	76522716
Number of paired-end alignments with a unique best hit:	47104705
Mapping efficiency:	61.6% 
Sequence pairs with no alignments under any condition:	17278917
Sequence pairs did not map uniquely:	12139094
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:	11756607	((converted) top strand)
GA/CT/CT:	11779525	(complementary to (converted) top strand)
GA/CT/GA:	11794325	(complementary to (converted) bottom strand)
CT/GA/GA:	11774173	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1636015607

Total methylated C's in CpG context:	22357746
Total methylated C's in CHG context:	1393584
Total methylated C's in CHH context:	5911899
Total methylated C's in Unknown context:	52609

Total unmethylated C's in CpG context:	191335494
Total unmethylated C's in CHG context:	285700905
Total unmethylated C's in CHH context:	1129315979
Total unmethylated C's in Unknown context:	3992567

C methylated in CpG context:	10.5%
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 6h 44m 13s