Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/16C_26psu_2_S14_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/16C_26psu_2_S14_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:	34160543
Number of paired-end alignments with a unique best hit:	13569314
Mapping efficiency:	39.7% 
Sequence pairs with no alignments under any condition:	14605510
Sequence pairs did not map uniquely:	5985719
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:	3462159	((converted) top strand)
GA/CT/CT:	3299311	(complementary to (converted) top strand)
GA/CT/GA:	3324231	(complementary to (converted) bottom strand)
CT/GA/GA:	3483613	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	519211274

Total methylated C's in CpG context:	39220245
Total methylated C's in CHG context:	887081
Total methylated C's in CHH context:	4786389
Total methylated C's in Unknown context:	104894

Total unmethylated C's in CpG context:	11228640
Total unmethylated C's in CHG context:	127769258
Total unmethylated C's in CHH context:	335319661
Total unmethylated C's in Unknown context:	445945

C methylated in CpG context:	77.7%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.4%
C methylated in unknown context (CN or CHN):	19.0%


Bismark completed in 0d 2h 0m 8s