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:	1000000
Number of paired-end alignments with a unique best hit:	613652
Mapping efficiency:	61.4% 
Sequence pairs with no alignments under any condition:	272246
Sequence pairs did not map uniquely:	114102
Sequence pairs which were discarded because genomic sequence could not be extracted:	5987

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	145203	((converted) top strand)
GA/CT/CT:	160011	(complementary to (converted) top strand)
GA/CT/GA:	158919	(complementary to (converted) bottom strand)
CT/GA/GA:	143532	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	27798661

Total methylated C's in CpG context:	388986
Total methylated C's in CHG context:	50661
Total methylated C's in CHH context:	177093
Total methylated C's in Unknown context:	3694

Total unmethylated C's in CpG context:	5713250
Total unmethylated C's in CHG context:	5412516
Total unmethylated C's in CHH context:	16056155
Total unmethylated C's in Unknown context:	51752

C methylated in CpG context:	6.4%
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 9m 19s