Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_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: 28731808 Number of paired-end alignments with a unique best hit: 17397580 Mapping efficiency: 60.6% Sequence pairs with no alignments under any condition: 6195835 Sequence pairs did not map uniquely: 5138393 Sequence pairs which were discarded because genomic sequence could not be extracted: 65502 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 8573754 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 8758324 ((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: 539984768 Total methylated C's in CpG context: 16925914 Total methylated C's in CHG context: 2727523 Total methylated C's in CHH context: 5571810 Total methylated C's in Unknown context: 180511 Total unmethylated C's in CpG context: 63148007 Total unmethylated C's in CHG context: 113347874 Total unmethylated C's in CHH context: 338263640 Total unmethylated C's in Unknown context: 2365499 C methylated in CpG context: 21.1% C methylated in CHG context: 2.3% C methylated in CHH context: 1.6% C methylated in unknown context (CN or CHN): 7.1% Bismark completed in 0d 6h 33m 5s