Bismark report for: input_1.fq (version: v0.22.1)
Option '--pbat' specified: alignments to original strands (OT and OB) strands were ignored (i.e. not performed)
Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmpuqE7r1/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet

Final Alignment report
======================
Sequences analysed in total:	44115
Number of alignments with a unique best hit from the different alignments:	13
Mapping efficiency:	0.0%
Sequences with no alignments under any condition:	44059
Sequences did not map uniquely:	43
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:	0	((converted) top strand)
CT/GA:	0	((converted) bottom strand)
GA/CT:	11	(complementary to (converted) top strand)
GA/GA:	2	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	307

Total methylated C's in CpG context:	1
Total methylated C's in CHG context:	3
Total methylated C's in CHH context:	227
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	1
Total unmethylated C's in CHG context:	4
Total unmethylated C's in CHH context:	71
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	50.0%
C methylated in CHG context:	42.9%
C methylated in CHH context:	76.2%
Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0


Bismark completed in 0d 0h 0m 7s