Bismark report for: input_1.fq (version: v0.22.1)
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmpVM2AEy/ 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:	1000
Number of alignments with a unique best hit from the different alignments:	8
Mapping efficiency:	0.8%
Sequences with no alignments under any condition:	983
Sequences did not map uniquely:	9
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:	6	((converted) top strand)
CT/GA:	2	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	143

Total methylated C's in CpG context:	3
Total methylated C's in CHG context:	2
Total methylated C's in CHH context:	3
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	1
Total unmethylated C's in CHG context:	36
Total unmethylated C's in CHH context:	98
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	75.0%
C methylated in CHG context:	5.3%
C methylated in CHH context:	3.0%
Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0


Bismark completed in 0d 0h 0m 5s