Bismark report for: /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth1_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth1_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:	49439
Mapping efficiency:	49.4% 
Sequence pairs with no alignments under any condition:	46001
Sequence pairs did not map uniquely:	4560
Sequence pairs which were discarded because genomic sequence could not be extracted:	213

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	11449	((converted) top strand)
GA/CT/CT:	12930	(complementary to (converted) top strand)
GA/CT/GA:	13090	(complementary to (converted) bottom strand)
CT/GA/GA:	11757	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2105037

Total methylated C's in CpG context:	15600
Total methylated C's in CHG context:	4256
Total methylated C's in CHH context:	16299
Total methylated C's in Unknown context:	880

Total unmethylated C's in CpG context:	305053
Total unmethylated C's in CHG context:	373438
Total unmethylated C's in CHH context:	1390391
Total unmethylated C's in Unknown context:	7283

C methylated in CpG context:	4.9%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	10.8%


Bismark completed in 0d 0h 4m 10s