Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_s456_trimmed.fq (version: v0.21.0) 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/sr320/data/olurida-genomes/v081/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals Final Alignment report ====================== Sequences analysed in total: 46792286 Number of alignments with a unique best hit from the different alignments: 14613325 Mapping efficiency: 31.2% Sequences with no alignments under any condition: 13908254 Sequences did not map uniquely: 18270707 Sequences which were discarded because genomic sequence could not be extracted: 13389 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3305147 ((converted) top strand) CT/GA: 3280126 ((converted) bottom strand) GA/CT: 4025896 (complementary to (converted) top strand) GA/GA: 3988767 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 88932661 Total methylated C's in CpG context: 11765630 Total methylated C's in CHG context: 420023 Total methylated C's in CHH context: 5013472 Total methylated C's in Unknown context: 2315 Total unmethylated C's in CpG context: 2476805 Total unmethylated C's in CHG context: 17514384 Total unmethylated C's in CHH context: 51742347 Total unmethylated C's in Unknown context: 15939 C methylated in CpG context: 82.6% C methylated in CHG context: 2.3% C methylated in CHH context: 8.8% C methylated in Unknown context (CN or CHN): 12.7% Bismark completed in 0d 1h 1m 47s