Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth12_R2_001_val_2.fq.gz (version: v0.21.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --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: 94422705 Number of paired-end alignments with a unique best hit: 3560 Mapping efficiency: 0.0% Sequence pairs with no alignments under any condition: 94419045 Sequence pairs did not map uniquely: 100 Sequence pairs which were discarded because genomic sequence could not be extracted: 34 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 813 ((converted) top strand) GA/CT/CT: 976 (complementary to (converted) top strand) GA/CT/GA: 942 (complementary to (converted) bottom strand) CT/GA/GA: 795 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 147541 Total methylated C's in CpG context: 5944 Total methylated C's in CHG context: 6442 Total methylated C's in CHH context: 12597 Total methylated C's in Unknown context: 88 Total unmethylated C's in CpG context: 30329 Total unmethylated C's in CHG context: 33847 Total unmethylated C's in CHH context: 58382 Total unmethylated C's in Unknown context: 347 C methylated in CpG context: 16.4% C methylated in CHG context: 16.0% C methylated in CHH context: 17.7% C methylated in unknown context (CN or CHN): 20.2% Bismark completed in 0d 1h 25m 14s