Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_2_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: 46105140 Number of alignments with a unique best hit from the different alignments: 14905949 Mapping efficiency: 32.3% Sequences with no alignments under any condition: 13855099 Sequences did not map uniquely: 17344092 Sequences which were discarded because genomic sequence could not be extracted: 12908 Number of sequences with unique best (first) alignment came from the bowtie output: CT/CT: 3323802 ((converted) top strand) CT/GA: 3303555 ((converted) bottom strand) GA/CT: 4149123 (complementary to (converted) top strand) GA/GA: 4116561 (complementary to (converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 89997267 Total methylated C's in CpG context: 11472605 Total methylated C's in CHG context: 410681 Total methylated C's in CHH context: 5226271 Total methylated C's in Unknown context: 2218 Total unmethylated C's in CpG context: 2334664 Total unmethylated C's in CHG context: 18029891 Total unmethylated C's in CHH context: 52523155 Total unmethylated C's in Unknown context: 15400 C methylated in CpG context: 83.1% C methylated in CHG context: 2.2% C methylated in CHH context: 9.0% C methylated in Unknown context (CN or CHN): 12.6% Bismark completed in 0d 1h 2m 19s