Bismark report for: /gscratch/srlab/sr320/data/cg-big/0502_R1.fastp.fq.gz and /gscratch/srlab/sr320/data/cg-big/0502_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:	58618241
Number of paired-end alignments with a unique best hit:	34683710
Mapping efficiency:	59.2% 
Sequence pairs with no alignments under any condition:	18011074
Sequence pairs did not map uniquely:	5923457
Sequence pairs which were discarded because genomic sequence could not be extracted:	122

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	17340208	((converted) top strand)
GA/CT/CT:	3654	(complementary to (converted) top strand)
GA/CT/GA:	4778	(complementary to (converted) bottom strand)
CT/GA/GA:	17334948	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1484454964

Total methylated C's in CpG context:	22326558
Total methylated C's in CHG context:	2339845
Total methylated C's in CHH context:	10359171
Total methylated C's in Unknown context:	188436

Total unmethylated C's in CpG context:	154228298
Total unmethylated C's in CHG context:	241093267
Total unmethylated C's in CHH context:	1054107825
Total unmethylated C's in Unknown context:	4382777

C methylated in CpG context:	12.6%
C methylated in CHG context:	1.0%
C methylated in CHH context:	1.0%
C methylated in unknown context (CN or CHN):	4.1%


Bismark completed in 0d 6h 19m 53s