Bismark report for: /gscratch/srlab/sr320/data/cvirg/36F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/36F_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: 163408505 Number of paired-end alignments with a unique best hit: 93893663 Mapping efficiency: 57.5% Sequence pairs with no alignments under any condition: 45977126 Sequence pairs did not map uniquely: 23537716 Sequence pairs which were discarded because genomic sequence could not be extracted: 1070 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 23677898 ((converted) top strand) GA/CT/CT: 23472350 (complementary to (converted) top strand) GA/CT/GA: 23271930 (complementary to (converted) bottom strand) CT/GA/GA: 23470415 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 3956409395 Total methylated C's in CpG context: 59938704 Total methylated C's in CHG context: 3056288 Total methylated C's in CHH context: 12809039 Total methylated C's in Unknown context: 275272 Total unmethylated C's in CpG context: 448891959 Total unmethylated C's in CHG context: 696190459 Total unmethylated C's in CHH context: 2735522946 Total unmethylated C's in Unknown context: 12801196 C methylated in CpG context: 11.8% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 2.1% Bismark completed in 0d 16h 21m 6s