Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Mc/Meth13.fastp-trim.202003062040_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Mc/Meth13.fastp-trim.202003062040_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:	98707822
Number of paired-end alignments with a unique best hit:	55417759
Mapping efficiency:	56.1% 
Sequence pairs with no alignments under any condition:	14281343
Sequence pairs did not map uniquely:	29008720
Sequence pairs which were discarded because genomic sequence could not be extracted:	415

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	13664437	((converted) top strand)
GA/CT/CT:	14080291	(complementary to (converted) top strand)
GA/CT/GA:	14058784	(complementary to (converted) bottom strand)
CT/GA/GA:	13613832	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2730281770

Total methylated C's in CpG context:	72681585
Total methylated C's in CHG context:	3919017
Total methylated C's in CHH context:	10017051
Total methylated C's in Unknown context:	64862

Total unmethylated C's in CpG context:	506801931
Total unmethylated C's in CHG context:	501441629
Total unmethylated C's in CHH context:	1635420557
Total unmethylated C's in Unknown context:	2886548

C methylated in CpG context:	12.5%
C methylated in CHG context:	0.8%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	2.2%


Bismark completed in 0d 9h 36m 12s