Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Pa/Meth8.fastp-trim.202003060943_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Pa/Meth8.fastp-trim.202003060943_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:	11892
Mapping efficiency:	11.9% 
Sequence pairs with no alignments under any condition:	87173
Sequence pairs did not map uniquely:	935
Sequence pairs which were discarded because genomic sequence could not be extracted:	7

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2988	((converted) top strand)
GA/CT/CT:	3036	(complementary to (converted) top strand)
GA/CT/GA:	3004	(complementary to (converted) bottom strand)
CT/GA/GA:	2857	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	541795

Total methylated C's in CpG context:	30803
Total methylated C's in CHG context:	1923
Total methylated C's in CHH context:	7874
Total methylated C's in Unknown context:	480

Total unmethylated C's in CpG context:	46486
Total unmethylated C's in CHG context:	99168
Total unmethylated C's in CHH context:	355541
Total unmethylated C's in Unknown context:	2118

C methylated in CpG context:	39.9%
C methylated in CHG context:	1.9%
C methylated in CHH context:	2.2%
C methylated in unknown context (CN or CHN):	18.5%


Bismark completed in 0d 0h 0m 22s