Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_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 -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: 22769546 Number of paired-end alignments with a unique best hit: 11176142 Mapping efficiency: 49.1% Sequence pairs with no alignments under any condition: 8105839 Sequence pairs did not map uniquely: 3487565 Sequence pairs which were discarded because genomic sequence could not be extracted: 63357 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5530376 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5582409 ((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: 336765537 Total methylated C's in CpG context: 10268810 Total methylated C's in CHG context: 1728174 Total methylated C's in CHH context: 7753782 Total methylated C's in Unknown context: 258944 Total unmethylated C's in CpG context: 37933764 Total unmethylated C's in CHG context: 72972330 Total unmethylated C's in CHH context: 206108677 Total unmethylated C's in Unknown context: 1762706 C methylated in CpG context: 21.3% C methylated in CHG context: 2.3% C methylated in CHH context: 3.6% C methylated in unknown context (CN or CHN): 12.8% Bismark completed in 0d 4h 9m 27s