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:	100000
Number of paired-end alignments with a unique best hit:	49035
Mapping efficiency:	49.0% 
Sequence pairs with no alignments under any condition:	47882
Sequence pairs did not map uniquely:	3083
Sequence pairs which were discarded because genomic sequence could not be extracted:	236

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	11441	((converted) top strand)
GA/CT/CT:	12819	(complementary to (converted) top strand)
GA/CT/GA:	13066	(complementary to (converted) bottom strand)
CT/GA/GA:	11473	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2166729

Total methylated C's in CpG context:	10636
Total methylated C's in CHG context:	4770
Total methylated C's in CHH context:	16989
Total methylated C's in Unknown context:	1240

Total unmethylated C's in CpG context:	321968
Total unmethylated C's in CHG context:	386743
Total unmethylated C's in CHH context:	1425623
Total unmethylated C's in Unknown context:	7758

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):	13.8%


Bismark completed in 0d 0h 1m 52s