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,-0.2 -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:	42014
Mapping efficiency:	42.0%
Sequences with no alignments under any condition:	36014
Sequences did not map uniquely:	21972
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:	10534	((converted) top strand)
CT/GA:	10547	((converted) bottom strand)
GA/CT:	10530	(complementary to (converted) top strand)
GA/GA:	10403	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	765495

Total methylated C's in CpG context:	59723
Total methylated C's in CHG context:	1155
Total methylated C's in CHH context:	6663
Total methylated C's in Unknown context:	66

Total unmethylated C's in CpG context:	17981
Total unmethylated C's in CHG context:	190257
Total unmethylated C's in CHH context:	489716
Total unmethylated C's in Unknown context:	417

C methylated in CpG context:	76.9%
C methylated in CHG context:	0.6%
C methylated in CHH context:	1.3%
C methylated in Unknown context (CN or CHN):	13.7%


Bismark completed in 0d 0h 0m 47s