Bismark report for: /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth5_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth5_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:	639003
Mapping efficiency:	63.9% 
Sequence pairs with no alignments under any condition:	241892
Sequence pairs did not map uniquely:	119105
Sequence pairs which were discarded because genomic sequence could not be extracted:	4356

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	150506	((converted) top strand)
GA/CT/CT:	166364	(complementary to (converted) top strand)
GA/CT/GA:	167167	(complementary to (converted) bottom strand)
CT/GA/GA:	150610	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	29305824

Total methylated C's in CpG context:	363041
Total methylated C's in CHG context:	44799
Total methylated C's in CHH context:	148913
Total methylated C's in Unknown context:	3893

Total unmethylated C's in CpG context:	6096770
Total unmethylated C's in CHG context:	5757922
Total unmethylated C's in CHH context:	16894379
Total unmethylated C's in Unknown context:	54649

C methylated in CpG context:	5.6%
C methylated in CHG context:	0.8%
C methylated in CHH context:	0.9%
C methylated in unknown context (CN or CHN):	6.6%


Bismark completed in 0d 0h 9m 37s