Bismark report for: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_4_R1_val_1_val_1_val_1.fq.gz and /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_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/Manchester/data/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ 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: 195404524 Number of paired-end alignments with a unique best hit: 122456913 Mapping efficiency: 62.7% Sequence pairs with no alignments under any condition: 43400673 Sequence pairs did not map uniquely: 29546938 Sequence pairs which were discarded because genomic sequence could not be extracted: 12448 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30724486 ((converted) top strand) GA/CT/CT: 30515064 (complementary to (converted) top strand) GA/CT/GA: 30491942 (complementary to (converted) bottom strand) CT/GA/GA: 30712973 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 4026686552 Total methylated C's in CpG context: 61517114 Total methylated C's in CHG context: 3775942 Total methylated C's in CHH context: 15774060 Total methylated C's in Unknown context: 162452 Total unmethylated C's in CpG context: 476713646 Total unmethylated C's in CHG context: 729091776 Total unmethylated C's in CHH context: 2739814014 Total unmethylated C's in Unknown context: 9663311 C methylated in CpG context: 11.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 1.7% Bismark completed in 0d 18h 42m 32s