Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Pa/Meth1.fastp-trim.202003061245_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Pa/Meth1.fastp-trim.202003061245_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:	72851576
Number of paired-end alignments with a unique best hit:	307226
Mapping efficiency:	0.4% 
Sequence pairs with no alignments under any condition:	72525273
Sequence pairs did not map uniquely:	19077
Sequence pairs which were discarded because genomic sequence could not be extracted:	1372

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	71554	((converted) top strand)
GA/CT/CT:	80775	(complementary to (converted) top strand)
GA/CT/GA:	81579	(complementary to (converted) bottom strand)
CT/GA/GA:	71946	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	13571525

Total methylated C's in CpG context:	67929
Total methylated C's in CHG context:	29960
Total methylated C's in CHH context:	105709
Total methylated C's in Unknown context:	8061

Total unmethylated C's in CpG context:	2015111
Total unmethylated C's in CHG context:	2432486
Total unmethylated C's in CHH context:	8920330
Total unmethylated C's in Unknown context:	46818

C methylated in CpG context:	3.3%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	14.7%


Bismark completed in 0d 0h 25m 26s