Bismark report for: /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth2_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth2_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:	84959218
Number of paired-end alignments with a unique best hit:	44949857
Mapping efficiency:	52.9% 
Sequence pairs with no alignments under any condition:	35329911
Sequence pairs did not map uniquely:	4679450
Sequence pairs which were discarded because genomic sequence could not be extracted:	175620

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	10477481	((converted) top strand)
GA/CT/CT:	11846403	(complementary to (converted) top strand)
GA/CT/GA:	11920218	(complementary to (converted) bottom strand)
CT/GA/GA:	10530135	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1859574363

Total methylated C's in CpG context:	15380726
Total methylated C's in CHG context:	3993349
Total methylated C's in CHH context:	15589463
Total methylated C's in Unknown context:	753013

Total unmethylated C's in CpG context:	270926838
Total unmethylated C's in CHG context:	334717510
Total unmethylated C's in CHH context:	1218966477
Total unmethylated C's in Unknown context:	6057639

C methylated in CpG context:	5.4%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	11.1%


Bismark completed in 0d 7h 31m 19s