Bismark report for: /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth6_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth6_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:	100000
Number of paired-end alignments with a unique best hit:	61747
Mapping efficiency:	61.7% 
Sequence pairs with no alignments under any condition:	27011
Sequence pairs did not map uniquely:	11242
Sequence pairs which were discarded because genomic sequence could not be extracted:	572

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	14685	((converted) top strand)
GA/CT/CT:	16026	(complementary to (converted) top strand)
GA/CT/GA:	16010	(complementary to (converted) bottom strand)
CT/GA/GA:	14454	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2796390

Total methylated C's in CpG context:	38601
Total methylated C's in CHG context:	4940
Total methylated C's in CHH context:	17551
Total methylated C's in Unknown context:	376

Total unmethylated C's in CpG context:	573516
Total unmethylated C's in CHG context:	544049
Total unmethylated C's in CHH context:	1617733
Total unmethylated C's in Unknown context:	5233

C methylated in CpG context:	6.3%
C methylated in CHG context:	0.9%
C methylated in CHH context:	1.1%
C methylated in unknown context (CN or CHN):	6.7%


Bismark completed in 0d 0h 4m 13s