Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Pa/Meth2.fastp-trim.202003062630_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Pa/Meth2.fastp-trim.202003062630_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Pdam_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:	83250476
Number of paired-end alignments with a unique best hit:	7456720
Mapping efficiency:	9.0% 
Sequence pairs with no alignments under any condition:	75525880
Sequence pairs did not map uniquely:	267876
Sequence pairs which were discarded because genomic sequence could not be extracted:	2786

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1746089	((converted) top strand)
GA/CT/CT:	1978861	(complementary to (converted) top strand)
GA/CT/GA:	1980469	(complementary to (converted) bottom strand)
CT/GA/GA:	1748515	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	320124616

Total methylated C's in CpG context:	1490490
Total methylated C's in CHG context:	732469
Total methylated C's in CHH context:	2668293
Total methylated C's in Unknown context:	166679

Total unmethylated C's in CpG context:	47936200
Total unmethylated C's in CHG context:	58087264
Total unmethylated C's in CHH context:	209209900
Total unmethylated C's in Unknown context:	1132871

C methylated in CpG context:	3.0%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	12.8%


Bismark completed in 0d 1h 35m 39s