Bismark report for: 16C_32psu_4_S4_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,-0.5 -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:	52522
Mapping efficiency:	52.5%
Sequences with no alignments under any condition:	29928
Sequences did not map uniquely:	17550
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:	12594	((converted) top strand)
CT/GA:	12512	((converted) bottom strand)
GA/CT:	13658	(complementary to (converted) top strand)
GA/GA:	13758	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1113857

Total methylated C's in CpG context:	74566
Total methylated C's in CHG context:	2348
Total methylated C's in CHH context:	13546
Total methylated C's in Unknown context:	796

Total unmethylated C's in CpG context:	24304
Total unmethylated C's in CHG context:	261579
Total unmethylated C's in CHH context:	737514
Total unmethylated C's in Unknown context:	3137

C methylated in CpG context:	75.4%
C methylated in CHG context:	0.9%
C methylated in CHH context:	1.8%
C methylated in Unknown context (CN or CHN):	20.2%


Bismark completed in 0d 0h 1m 32s