Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-111_S29_L005_R2_001_val_2.fq.gz (version: v0.19.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Pgenr/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) Final Alignment report ====================== Sequence pairs analysed in total: 27014996 Number of paired-end alignments with a unique best hit: 16766118 Mapping efficiency: 62.1% Sequence pairs with no alignments under any condition: 5610754 Sequence pairs did not map uniquely: 4638124 Sequence pairs which were discarded because genomic sequence could not be extracted: 65156 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 8299941 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 8401021 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 524809948 Total methylated C's in CpG context: 15833281 Total methylated C's in CHG context: 2489514 Total methylated C's in CHH context: 5221626 Total methylated C's in Unknown context: 168237 Total unmethylated C's in CpG context: 58351105 Total unmethylated C's in CHG context: 109756813 Total unmethylated C's in CHH context: 333157609 Total unmethylated C's in Unknown context: 2261184 C methylated in CpG context: 21.3% C methylated in CHG context: 2.2% C methylated in CHH context: 1.5% C methylated in unknown context (CN or CHN): 6.9% Bismark completed in 0d 6h 19m 48s