Bismark report for: /gscratch/srlab/sr320/data/froger/trim/Pa/Meth4.fastp-trim.202003062011_R1_001.fastq.gz and /gscratch/srlab/sr320/data/froger/trim/Pa/Meth4.fastp-trim.202003062011_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:	146726267
Number of paired-end alignments with a unique best hit:	40217655
Mapping efficiency:	27.4% 
Sequence pairs with no alignments under any condition:	101010131
Sequence pairs did not map uniquely:	5498481
Sequence pairs which were discarded because genomic sequence could not be extracted:	20680

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	9915568	((converted) top strand)
GA/CT/CT:	10354638	(complementary to (converted) top strand)
GA/CT/GA:	10209566	(complementary to (converted) bottom strand)
CT/GA/GA:	9717203	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1749438713

Total methylated C's in CpG context:	43710315
Total methylated C's in CHG context:	4930932
Total methylated C's in CHH context:	12331107
Total methylated C's in Unknown context:	206187

Total unmethylated C's in CpG context:	334058971
Total unmethylated C's in CHG context:	338863365
Total unmethylated C's in CHH context:	1015544023
Total unmethylated C's in Unknown context:	3574152

C methylated in CpG context:	11.6%
C methylated in CHG context:	1.4%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	5.5%


Bismark completed in 0d 6h 44m 5s