Bismark report for: CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz (version: v0.19.0)
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
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,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	100000
Number of alignments with a unique best hit from the different alignments:	44737
Mapping efficiency:	44.7%
Sequences with no alignments under any condition:	36795
Sequences did not map uniquely:	18468
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	10318	((converted) top strand)
CT/GA:	10397	((converted) bottom strand)
GA/CT:	12109	(complementary to (converted) top strand)
GA/GA:	11913	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	870157

Total methylated C's in CpG context:	60251
Total methylated C's in CHG context:	1300
Total methylated C's in CHH context:	6664
Total methylated C's in Unknown context:	73

Total unmethylated C's in CpG context:	17898
Total unmethylated C's in CHG context:	200778
Total unmethylated C's in CHH context:	583266
Total unmethylated C's in Unknown context:	479

C methylated in CpG context:	77.1%
C methylated in CHG context:	0.6%
C methylated in CHH context:	1.1%
C methylated in Unknown context (CN or CHN):	13.2%


Bismark completed in 0d 0h 1m 24s