Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_14_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_14_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: 36340861 Number of paired-end alignments with a unique best hit: 22341478 Mapping efficiency: 61.5% Sequence pairs with no alignments under any condition: 8183804 Sequence pairs did not map uniquely: 5815579 Sequence pairs which were discarded because genomic sequence could not be extracted: 79 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5552803 ((converted) top strand) GA/CT/CT: 5596286 (complementary to (converted) top strand) GA/CT/GA: 5618114 (complementary to (converted) bottom strand) CT/GA/GA: 5574196 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 788907403 Total methylated C's in CpG context: 11967003 Total methylated C's in CHG context: 694010 Total methylated C's in CHH context: 2844733 Total methylated C's in Unknown context: 29476 Total unmethylated C's in CpG context: 89548490 Total unmethylated C's in CHG context: 136421293 Total unmethylated C's in CHH context: 547431874 Total unmethylated C's in Unknown context: 1911810 C methylated in CpG context: 11.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 3h 31m 50s