Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Mc/Meth15.fastp-trim.202003065503_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Mc/Meth15.fastp-trim.202003065503_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:	100000000
Number of paired-end alignments with a unique best hit:	53148550
Mapping efficiency:	53.1% 
Sequence pairs with no alignments under any condition:	15564204
Sequence pairs did not map uniquely:	31287246
Sequence pairs which were discarded because genomic sequence could not be extracted:	367

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	12843923	((converted) top strand)
GA/CT/CT:	13723742	(complementary to (converted) top strand)
GA/CT/GA:	13736475	(complementary to (converted) bottom strand)
CT/GA/GA:	12844043	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2543980988

Total methylated C's in CpG context:	72241382
Total methylated C's in CHG context:	5440664
Total methylated C's in CHH context:	14488776
Total methylated C's in Unknown context:	81069

Total unmethylated C's in CpG context:	475981494
Total unmethylated C's in CHG context:	469693006
Total unmethylated C's in CHH context:	1506135666
Total unmethylated C's in Unknown context:	2701046

C methylated in CpG context:	13.2%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.0%
C methylated in unknown context (CN or CHN):	2.9%


Bismark completed in 0d 9h 11m 13s