Bismark report for: /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth8_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/041720-pan-u/Pact_trim/Meth8_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:	50248
Mapping efficiency:	50.2% 
Sequence pairs with no alignments under any condition:	43383
Sequence pairs did not map uniquely:	6369
Sequence pairs which were discarded because genomic sequence could not be extracted:	147

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	12176	((converted) top strand)
GA/CT/CT:	12652	(complementary to (converted) top strand)
GA/CT/GA:	13038	(complementary to (converted) bottom strand)
CT/GA/GA:	12235	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2362246

Total methylated C's in CpG context:	289097
Total methylated C's in CHG context:	11578
Total methylated C's in CHH context:	34199
Total methylated C's in Unknown context:	1726

Total unmethylated C's in CpG context:	74819
Total unmethylated C's in CHG context:	455380
Total unmethylated C's in CHH context:	1497173
Total unmethylated C's in Unknown context:	7374

C methylated in CpG context:	79.4%
C methylated in CHG context:	2.5%
C methylated in CHH context:	2.2%
C methylated in unknown context (CN or CHN):	19.0%


Bismark completed in 0d 0h 4m 11s