Bismark report for: /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fastp.fq.gz (version: v0.22.3)
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 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:	100000
Number of paired-end alignments with a unique best hit:	62089
Mapping efficiency:	62.1% 
Sequence pairs with no alignments under any condition:	21390
Sequence pairs did not map uniquely:	16521
Sequence pairs which were discarded because genomic sequence could not be extracted:	1

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	15451	((converted) top strand)
GA/CT/CT:	15505	(complementary to (converted) top strand)
GA/CT/GA:	15794	(complementary to (converted) bottom strand)
CT/GA/GA:	15338	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2178029

Total methylated C's in CpG context:	32720
Total methylated C's in CHG context:	1899
Total methylated C's in CHH context:	7658
Total methylated C's in Unknown context:	85

Total unmethylated C's in CpG context:	246804
Total unmethylated C's in CHG context:	376144
Total unmethylated C's in CHH context:	1512804
Total unmethylated C's in Unknown context:	5234

C methylated in CpG context:	11.7%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	1.6%


Bismark completed in 0d 0h 0m 49s