Bismark report for: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_1_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_1_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: 50993451 Number of paired-end alignments with a unique best hit: 31434721 Mapping efficiency: 61.6% Sequence pairs with no alignments under any condition: 11134052 Sequence pairs did not map uniquely: 8424678 Sequence pairs which were discarded because genomic sequence could not be extracted: 115 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 7891335 ((converted) top strand) GA/CT/CT: 7795639 (complementary to (converted) top strand) GA/CT/GA: 7818927 (complementary to (converted) bottom strand) CT/GA/GA: 7928705 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1113134972 Total methylated C's in CpG context: 13763919 Total methylated C's in CHG context: 897841 Total methylated C's in CHH context: 3720045 Total methylated C's in Unknown context: 35255 Total unmethylated C's in CpG context: 131347662 Total unmethylated C's in CHG context: 194126289 Total unmethylated C's in CHH context: 769279216 Total unmethylated C's in Unknown context: 2644308 C methylated in CpG context: 9.5% 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 56m 59s