Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_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: 30015261 Number of paired-end alignments with a unique best hit: 18880850 Mapping efficiency: 62.9% Sequence pairs with no alignments under any condition: 5947034 Sequence pairs did not map uniquely: 5187377 Sequence pairs which were discarded because genomic sequence could not be extracted: 61439 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 9381792 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 9437619 ((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: 589822412 Total methylated C's in CpG context: 18751306 Total methylated C's in CHG context: 2772707 Total methylated C's in CHH context: 6568341 Total methylated C's in Unknown context: 206436 Total unmethylated C's in CpG context: 62277020 Total unmethylated C's in CHG context: 124556422 Total unmethylated C's in CHH context: 374896616 Total unmethylated C's in Unknown context: 2853303 C methylated in CpG context: 23.1% C methylated in CHG context: 2.2% C methylated in CHH context: 1.7% C methylated in unknown context (CN or CHN): 6.7% Bismark completed in 0d 7h 5m 40s