Bismark report for: 16C_26psu_1_S13_R1_001_val_1.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:	41443
Mapping efficiency:	41.4%
Sequences with no alignments under any condition:	39661
Sequences did not map uniquely:	18896
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:	10122	((converted) top strand)
CT/GA:	10203	((converted) bottom strand)
GA/CT:	10507	(complementary to (converted) top strand)
GA/GA:	10611	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	811452

Total methylated C's in CpG context:	61638
Total methylated C's in CHG context:	1250
Total methylated C's in CHH context:	6314
Total methylated C's in Unknown context:	81

Total unmethylated C's in CpG context:	18623
Total unmethylated C's in CHG context:	198495
Total unmethylated C's in CHH context:	525132
Total unmethylated C's in Unknown context:	459

C methylated in CpG context:	76.8%
C methylated in CHG context:	0.6%
C methylated in CHH context:	1.2%
C methylated in Unknown context (CN or CHN):	15.0%


Bismark completed in 0d 0h 0m 49s