Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_2_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_2_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: 55025914 Number of paired-end alignments with a unique best hit: 33388393 Mapping efficiency: 60.7% Sequence pairs with no alignments under any condition: 12972059 Sequence pairs did not map uniquely: 8665462 Sequence pairs which were discarded because genomic sequence could not be extracted: 120 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 8328453 ((converted) top strand) GA/CT/CT: 8319972 (complementary to (converted) top strand) GA/CT/GA: 8363956 (complementary to (converted) bottom strand) CT/GA/GA: 8375892 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1195501862 Total methylated C's in CpG context: 15540506 Total methylated C's in CHG context: 983606 Total methylated C's in CHH context: 4120629 Total methylated C's in Unknown context: 38661 Total unmethylated C's in CpG context: 139270636 Total unmethylated C's in CHG context: 205694628 Total unmethylated C's in CHH context: 829891857 Total unmethylated C's in Unknown context: 2941456 C methylated in CpG context: 10.0% 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 5h 21m 24s