Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Mc/Meth10.fastp-trim.202003063900_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Mc/Meth10.fastp-trim.202003063900_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Mcap_Genome/ 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:	81884259
Number of paired-end alignments with a unique best hit:	16579465
Mapping efficiency:	20.2% 
Sequence pairs with no alignments under any condition:	58817192
Sequence pairs did not map uniquely:	6487602
Sequence pairs which were discarded because genomic sequence could not be extracted:	292

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3888257	((converted) top strand)
GA/CT/CT:	4389764	(complementary to (converted) top strand)
GA/CT/GA:	4405867	(complementary to (converted) bottom strand)
CT/GA/GA:	3895285	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	766727977

Total methylated C's in CpG context:	15597730
Total methylated C's in CHG context:	1943098
Total methylated C's in CHH context:	6551324
Total methylated C's in Unknown context:	550110

Total unmethylated C's in CpG context:	113974264
Total unmethylated C's in CHG context:	135674473
Total unmethylated C's in CHH context:	492987088
Total unmethylated C's in Unknown context:	2355958

C methylated in CpG context:	12.0%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	18.9%


Bismark completed in 0d 3h 17m 2s