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:	284116370
Number of paired-end alignments with a unique best hit:	181427646
Mapping efficiency:	63.9% 
Sequence pairs with no alignments under any condition:	68552902
Sequence pairs did not map uniquely:	34135822
Sequence pairs which were discarded because genomic sequence could not be extracted:	1236735

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	42968517	((converted) top strand)
GA/CT/CT:	47095015	(complementary to (converted) top strand)
GA/CT/GA:	47244227	(complementary to (converted) bottom strand)
CT/GA/GA:	42883152	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	8278073563

Total methylated C's in CpG context:	103088093
Total methylated C's in CHG context:	12751693
Total methylated C's in CHH context:	42521811
Total methylated C's in Unknown context:	1099911

Total unmethylated C's in CpG context:	1724103076
Total unmethylated C's in CHG context:	1627995440
Total unmethylated C's in CHH context:	4767613450
Total unmethylated C's in Unknown context:	15496450

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 1d 4h 42m 0s