Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-153_S4_L002_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: 26009397 Number of paired-end alignments with a unique best hit: 15982489 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 5193977 Sequence pairs did not map uniquely: 4832931 Sequence pairs which were discarded because genomic sequence could not be extracted: 108237 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6934507 ((converted) top strand) GA/CT/CT: 654156 (complementary to (converted) top strand) GA/CT/GA: 666992 (complementary to (converted) bottom strand) CT/GA/GA: 7618597 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 505355949 Total methylated C's in CpG context: 15025546 Total methylated C's in CHG context: 2732936 Total methylated C's in CHH context: 27681789 Total methylated C's in Unknown context: 985352 Total unmethylated C's in CpG context: 59779306 Total unmethylated C's in CHG context: 103860099 Total unmethylated C's in CHH context: 296276273 Total unmethylated C's in Unknown context: 2935213 C methylated in CpG context: 20.1% C methylated in CHG context: 2.6% C methylated in CHH context: 8.5% C methylated in unknown context (CN or CHN): 25.1% Bismark completed in 0d 7h 32m 6s