Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_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: 74531056 Number of alignments with a unique best hit from the different alignments: 21379604 Mapping efficiency: 28.7% Sequences with no alignments under any condition: 22542289 Sequences did not map uniquely: 30609163 Sequences which were discarded because genomic sequence could not be extracted: 23016 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 4899455 ((converted) top strand) CT/GA: 4865445 ((converted) bottom strand) GA/CT: 5819536 (complementary to (converted) top strand) GA/GA: 5772152 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 134402420 Total methylated C's in CpG context: 22135048 Total methylated C's in CHG context: 633998 Total methylated C's in CHH context: 7135489 Total methylated C's in Unknown context: 4243 Total unmethylated C's in CpG context: 3717836 Total unmethylated C's in CHG context: 26058014 Total unmethylated C's in CHH context: 74722035 Total unmethylated C's in Unknown context: 26107 C methylated in CpG context: 85.6% C methylated in CHG context: 2.4% C methylated in CHH context: 8.7% C methylated in Unknown context (CN or CHN): 14.0% Bismark completed in 0d 1h 34m 37s