Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_4_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_4_R2_val_2_val_2_val_2.fq.gz (version: v0.22.3) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/yaaminiv/Hawes/data/Cg-roslin/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB) Final Alignment report ====================== Sequence pairs analysed in total: 49306248 Number of paired-end alignments with a unique best hit: 29947855 Mapping efficiency: 60.7% Sequence pairs with no alignments under any condition: 11369491 Sequence pairs did not map uniquely: 7988902 Sequence pairs which were discarded because genomic sequence could not be extracted: 134 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 7489798 ((converted) top strand) GA/CT/CT: 7474853 (complementary to (converted) top strand) GA/CT/GA: 7478087 (complementary to (converted) bottom strand) CT/GA/GA: 7504983 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1061581694 Total methylated C's in CpG context: 13679546 Total methylated C's in CHG context: 850507 Total methylated C's in CHH context: 3492407 Total methylated C's in Unknown context: 35439 Total unmethylated C's in CpG context: 121952808 Total unmethylated C's in CHG context: 181799911 Total unmethylated C's in CHH context: 739806515 Total unmethylated C's in Unknown context: 2616781 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 4h 45m 30s