Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Pa/Meth9.fastp-trim.202003062409_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Pa/Meth9.fastp-trim.202003062409_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Pact_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:	32972
Mapping efficiency:	33.0% 
Sequence pairs with no alignments under any condition:	64506
Sequence pairs did not map uniquely:	2522
Sequence pairs which were discarded because genomic sequence could not be extracted:	210

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8027	((converted) top strand)
GA/CT/CT:	8397	(complementary to (converted) top strand)
GA/CT/GA:	8259	(complementary to (converted) bottom strand)
CT/GA/GA:	8079	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1437369

Total methylated C's in CpG context:	41310
Total methylated C's in CHG context:	4480
Total methylated C's in CHH context:	15680
Total methylated C's in Unknown context:	1252

Total unmethylated C's in CpG context:	164156
Total unmethylated C's in CHG context:	265027
Total unmethylated C's in CHH context:	946716
Total unmethylated C's in Unknown context:	5534

C methylated in CpG context:	20.1%
C methylated in CHG context:	1.7%
C methylated in CHH context:	1.6%
C methylated in unknown context (CN or CHN):	18.4%


Bismark completed in 0d 0h 1m 43s