Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/16C_32psu_2_S2_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/16C_32psu_2_S2_R2_001_val_2.fq.gz (version: v0.22.3)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -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:	35076228
Number of paired-end alignments with a unique best hit:	15319099
Mapping efficiency:	43.7% 
Sequence pairs with no alignments under any condition:	12582127
Sequence pairs did not map uniquely:	7175002
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	4095981	((converted) top strand)
GA/CT/CT:	3522702	(complementary to (converted) top strand)
GA/CT/GA:	3558665	(complementary to (converted) bottom strand)
CT/GA/GA:	4141751	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	539720304

Total methylated C's in CpG context:	41055352
Total methylated C's in CHG context:	964874
Total methylated C's in CHH context:	5679764
Total methylated C's in Unknown context:	110537

Total unmethylated C's in CpG context:	12540448
Total unmethylated C's in CHG context:	134466169
Total unmethylated C's in CHH context:	345013697
Total unmethylated C's in Unknown context:	429502

C methylated in CpG context:	76.6%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.6%
C methylated in unknown context (CN or CHN):	20.5%


Bismark completed in 0d 2h 4m 42s