Bismark report for: 16C_26psu_1_S13_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:	49466
Mapping efficiency:	49.5%
Sequences with no alignments under any condition:	28942
Sequences did not map uniquely:	21592
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:	11492	((converted) top strand)
CT/GA:	11527	((converted) bottom strand)
GA/CT:	13171	(complementary to (converted) top strand)
GA/GA:	13276	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	983426

Total methylated C's in CpG context:	72761
Total methylated C's in CHG context:	2146
Total methylated C's in CHH context:	14523
Total methylated C's in Unknown context:	770

Total unmethylated C's in CpG context:	23553
Total unmethylated C's in CHG context:	237326
Total unmethylated C's in CHH context:	633117
Total unmethylated C's in Unknown context:	2792

C methylated in CpG context:	75.5%
C methylated in CHG context:	0.9%
C methylated in CHH context:	2.2%
C methylated in Unknown context (CN or CHN):	21.6%


Bismark completed in 0d 0h 1m 29s