Bismark report for: /gscratch/srlab/sr320/data/cvirg/44F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/44F_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: 308919236 Number of paired-end alignments with a unique best hit: 175961500 Mapping efficiency: 57.0% Sequence pairs with no alignments under any condition: 88375390 Sequence pairs did not map uniquely: 44582346 Sequence pairs which were discarded because genomic sequence could not be extracted: 933 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 44288358 ((converted) top strand) GA/CT/CT: 43850154 (complementary to (converted) top strand) GA/CT/GA: 43681468 (complementary to (converted) bottom strand) CT/GA/GA: 44140587 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 7480514122 Total methylated C's in CpG context: 109273103 Total methylated C's in CHG context: 5254054 Total methylated C's in CHH context: 21855128 Total methylated C's in Unknown context: 475606 Total unmethylated C's in CpG context: 845598808 Total unmethylated C's in CHG context: 1308578802 Total unmethylated C's in CHH context: 5189954227 Total unmethylated C's in Unknown context: 24907669 C methylated in CpG context: 11.4% C methylated in CHG context: 0.4% C methylated in CHH context: 0.4% C methylated in unknown context (CN or CHN): 1.9% Bismark completed in 1d 6h 58m 25s