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