Bismark report for: 8C_32psu_3_S7_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,-0.3 -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:	45202
Mapping efficiency:	45.2%
Sequences with no alignments under any condition:	31441
Sequences did not map uniquely:	23357
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:	11371	((converted) top strand)
CT/GA:	11344	((converted) bottom strand)
GA/CT:	11308	(complementary to (converted) top strand)
GA/GA:	11179	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	827688

Total methylated C's in CpG context:	64114
Total methylated C's in CHG context:	1392
Total methylated C's in CHH context:	8627
Total methylated C's in Unknown context:	197

Total unmethylated C's in CpG context:	19733
Total unmethylated C's in CHG context:	205663
Total unmethylated C's in CHH context:	528159
Total unmethylated C's in Unknown context:	890

C methylated in CpG context:	76.5%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.6%
C methylated in Unknown context (CN or CHN):	18.1%


Bismark completed in 0d 0h 0m 47s