Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Mc/Meth17.fastp-trim.202003063731_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Mc/Meth17.fastp-trim.202003063731_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:	78388365
Number of paired-end alignments with a unique best hit:	19359825
Mapping efficiency:	24.7% 
Sequence pairs with no alignments under any condition:	50604520
Sequence pairs did not map uniquely:	8424020
Sequence pairs which were discarded because genomic sequence could not be extracted:	273

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4748276	((converted) top strand)
GA/CT/CT:	4917675	(complementary to (converted) top strand)
GA/CT/GA:	4920678	(complementary to (converted) bottom strand)
CT/GA/GA:	4772923	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	873966140

Total methylated C's in CpG context:	21218332
Total methylated C's in CHG context:	2381255
Total methylated C's in CHH context:	8173030
Total methylated C's in Unknown context:	786259

Total unmethylated C's in CpG context:	129235842
Total unmethylated C's in CHG context:	154077043
Total unmethylated C's in CHH context:	558880638
Total unmethylated C's in Unknown context:	2896344

C methylated in CpG context:	14.1%
C methylated in CHG context:	1.5%
C methylated in CHH context:	1.4%
C methylated in unknown context (CN or CHN):	21.4%


Bismark completed in 0d 4h 2m 20s