Bismark report for: /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth4_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth4_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:	60630
Mapping efficiency:	60.6% 
Sequence pairs with no alignments under any condition:	27923
Sequence pairs did not map uniquely:	11447
Sequence pairs which were discarded because genomic sequence could not be extracted:	603

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	14325	((converted) top strand)
GA/CT/CT:	15556	(complementary to (converted) top strand)
GA/CT/GA:	15685	(complementary to (converted) bottom strand)
CT/GA/GA:	14461	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2740471

Total methylated C's in CpG context:	35671
Total methylated C's in CHG context:	5551
Total methylated C's in CHH context:	19320
Total methylated C's in Unknown context:	374

Total unmethylated C's in CpG context:	569701
Total unmethylated C's in CHG context:	539060
Total unmethylated C's in CHH context:	1571168
Total unmethylated C's in Unknown context:	5073

C methylated in CpG context:	5.9%
C methylated in CHG context:	1.0%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	6.9%


Bismark completed in 0d 0h 4m 15s