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/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:	72851576
Number of paired-end alignments with a unique best hit:	29909743
Mapping efficiency:	41.1% 
Sequence pairs with no alignments under any condition:	41941712
Sequence pairs did not map uniquely:	1000121
Sequence pairs which were discarded because genomic sequence could not be extracted:	15036

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7000099	((converted) top strand)
GA/CT/CT:	7937526	(complementary to (converted) top strand)
GA/CT/GA:	7944576	(complementary to (converted) bottom strand)
CT/GA/GA:	7012506	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1314570373

Total methylated C's in CpG context:	6308155
Total methylated C's in CHG context:	2922305
Total methylated C's in CHH context:	10444004
Total methylated C's in Unknown context:	743676

Total unmethylated C's in CpG context:	194808095
Total unmethylated C's in CHG context:	236105269
Total unmethylated C's in CHH context:	863982545
Total unmethylated C's in Unknown context:	4755326

C methylated in CpG context:	3.1%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	13.5%


Bismark completed in 0d 5h 23m 5s