Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Pa/Meth3.fastp-trim.202003064031_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Pa/Meth3.fastp-trim.202003064031_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:	100000
Number of paired-end alignments with a unique best hit:	39540
Mapping efficiency:	39.5% 
Sequence pairs with no alignments under any condition:	59056
Sequence pairs did not map uniquely:	1404
Sequence pairs which were discarded because genomic sequence could not be extracted:	19

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	9337	((converted) top strand)
GA/CT/CT:	10383	(complementary to (converted) top strand)
GA/CT/GA:	10474	(complementary to (converted) bottom strand)
CT/GA/GA:	9327	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1743548

Total methylated C's in CpG context:	8689
Total methylated C's in CHG context:	3922
Total methylated C's in CHH context:	13892
Total methylated C's in Unknown context:	967

Total unmethylated C's in CpG context:	260749
Total unmethylated C's in CHG context:	315223
Total unmethylated C's in CHH context:	1141073
Total unmethylated C's in Unknown context:	6526

C methylated in CpG context:	3.2%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	12.9%


Bismark completed in 0d 0h 1m 4s