Bismark report for: input_1.fq.gz (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/tmp53fiEn/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.8 --ignore-quals --quiet Final Alignment report ====================== Sequences analysed in total: 44115 Number of alignments with a unique best hit from the different alignments: 1992 Mapping efficiency: 4.5% Sequences with no alignments under any condition: 40786 Sequences did not map uniquely: 1337 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: 832 ((converted) top strand) CT/GA: 1160 ((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: 31956 Total methylated C's in CpG context: 564 Total methylated C's in CHG context: 249 Total methylated C's in CHH context: 882 Total methylated C's in Unknown context: 36 Total unmethylated C's in CpG context: 608 Total unmethylated C's in CHG context: 6183 Total unmethylated C's in CHH context: 23470 Total unmethylated C's in Unknown context: 232 C methylated in CpG context: 48.1% C methylated in CHG context: 3.9% C methylated in CHH context: 3.6% C methylated in Unknown context (CN or CHN): 13.4% Bismark completed in 0d 0h 0m 8s