Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_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 --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --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: 27792315 Number of paired-end alignments with a unique best hit: 17488047 Mapping efficiency: 62.9% Sequence pairs with no alignments under any condition: 5210436 Sequence pairs did not map uniquely: 5093832 Sequence pairs which were discarded because genomic sequence could not be extracted: 48457 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 8133934 ((converted) top strand) GA/CT/CT: 548533 (complementary to (converted) top strand) GA/CT/GA: 560296 (complementary to (converted) bottom strand) CT/GA/GA: 8196827 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 549203131 Total methylated C's in CpG context: 15344220 Total methylated C's in CHG context: 2892869 Total methylated C's in CHH context: 20865501 Total methylated C's in Unknown context: 826102 Total unmethylated C's in CpG context: 60423540 Total unmethylated C's in CHG context: 110053605 Total unmethylated C's in CHH context: 339623396 Total unmethylated C's in Unknown context: 2941806 C methylated in CpG context: 20.3% C methylated in CHG context: 2.6% C methylated in CHH context: 5.8% C methylated in unknown context (CN or CHN): 21.9% Bismark completed in 0d 8h 10m 42s