Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-175_S14_L003_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: 24654280 Number of paired-end alignments with a unique best hit: 14491765 Mapping efficiency: 58.8% Sequence pairs with no alignments under any condition: 6060084 Sequence pairs did not map uniquely: 4102431 Sequence pairs which were discarded because genomic sequence could not be extracted: 68350 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 7159820 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 7263595 ((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: 451575919 Total methylated C's in CpG context: 14340294 Total methylated C's in CHG context: 2142922 Total methylated C's in CHH context: 8297568 Total methylated C's in Unknown context: 250659 Total unmethylated C's in CpG context: 51171881 Total unmethylated C's in CHG context: 97528384 Total unmethylated C's in CHH context: 278094870 Total unmethylated C's in Unknown context: 2284707 C methylated in CpG context: 21.9% C methylated in CHG context: 2.1% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 9.9% Bismark completed in 0d 5h 31m 32s