Bismark report for: CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz and CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz (version: v0.19.0)
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,-0.6 -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:	50628
Mapping efficiency:	50.6% 
Sequence pairs with no alignments under any condition:	30726
Sequence pairs did not map uniquely:	18646
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:	12963	((converted) top strand)
GA/CT/CT:	12443	(complementary to (converted) top strand)
GA/CT/GA:	12537	(complementary to (converted) bottom strand)
CT/GA/GA:	12685	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1940689

Total methylated C's in CpG context:	132803
Total methylated C's in CHG context:	3999
Total methylated C's in CHH context:	24087
Total methylated C's in Unknown context:	1387


Total unmethylated C's in CpG context:	41489
Total unmethylated C's in CHG context:	453629
Total unmethylated C's in CHH context:	1284682
Total unmethylated C's in Unknown context:	5281


C methylated in CpG context:	76.2%
C methylated in CHG context:	0.9%
C methylated in CHH context:	1.8%
C methylated in unknown context (CN or CHN):	20.8%


Bismark completed in 0d 0h 0m 38s