Bismark report for: /gscratch/srlab/sr320/data/cvirg/19F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/19F_R2_val_2.fq.gz (version: v0.22.3) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cvirg-genome/ 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: 199653889 Number of paired-end alignments with a unique best hit: 111541442 Mapping efficiency: 55.9% Sequence pairs with no alignments under any condition: 57418948 Sequence pairs did not map uniquely: 30693499 Sequence pairs which were discarded because genomic sequence could not be extracted: 1380 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 28112102 ((converted) top strand) GA/CT/CT: 28046167 (complementary to (converted) top strand) GA/CT/GA: 27650327 (complementary to (converted) bottom strand) CT/GA/GA: 27731466 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 4485323711 Total methylated C's in CpG context: 71722745 Total methylated C's in CHG context: 3518077 Total methylated C's in CHH context: 15860797 Total methylated C's in Unknown context: 363361 Total unmethylated C's in CpG context: 522766214 Total unmethylated C's in CHG context: 810110614 Total unmethylated C's in CHH context: 3061345264 Total unmethylated C's in Unknown context: 14348391 C methylated in CpG context: 12.1% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 2.5% Bismark completed in 0d 19h 7m 0s