Bismark report for: /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth2_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth2_R2_001_val_2.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Pan_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:	1000000
Number of paired-end alignments with a unique best hit:	527972
Mapping efficiency:	52.8% 
Sequence pairs with no alignments under any condition:	417431
Sequence pairs did not map uniquely:	54597
Sequence pairs which were discarded because genomic sequence could not be extracted:	2086

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	122467	((converted) top strand)
GA/CT/CT:	139896	(complementary to (converted) top strand)
GA/CT/GA:	139708	(complementary to (converted) bottom strand)
CT/GA/GA:	123815	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	21892246

Total methylated C's in CpG context:	179264
Total methylated C's in CHG context:	46239
Total methylated C's in CHH context:	183060
Total methylated C's in Unknown context:	9061

Total unmethylated C's in CpG context:	3188337
Total unmethylated C's in CHG context:	3941892
Total unmethylated C's in CHH context:	14353454
Total unmethylated C's in Unknown context:	71111

C methylated in CpG context:	5.3%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	11.3%


Bismark completed in 0d 0h 8m 54s