Bismark report for: /gscratch/srlab/sr320/data/cg/zr3534_5_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_5_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:	84046138
Number of paired-end alignments with a unique best hit:	51605460
Mapping efficiency:	61.4% 
Sequence pairs with no alignments under any condition:	18775249
Sequence pairs did not map uniquely:	13665429
Sequence pairs which were discarded because genomic sequence could not be extracted:	131

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	12883364	((converted) top strand)
GA/CT/CT:	12873781	(complementary to (converted) top strand)
GA/CT/GA:	12919828	(complementary to (converted) bottom strand)
CT/GA/GA:	12928356	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1797447404

Total methylated C's in CpG context:	26305415
Total methylated C's in CHG context:	1561214
Total methylated C's in CHH context:	6629878
Total methylated C's in Unknown context:	63671

Total unmethylated C's in CpG context:	207531853
Total unmethylated C's in CHG context:	312507188
Total unmethylated C's in CHH context:	1242911856
Total unmethylated C's in Unknown context:	4404409

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 17h 34m 18s