Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Meth18_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: 61585400 Number of paired-end alignments with a unique best hit: 19475 Mapping efficiency: 0.0% Sequence pairs with no alignments under any condition: 61565719 Sequence pairs did not map uniquely: 206 Sequence pairs which were discarded because genomic sequence could not be extracted: 290 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4204 ((converted) top strand) GA/CT/CT: 5404 (complementary to (converted) top strand) GA/CT/GA: 5427 (complementary to (converted) bottom strand) CT/GA/GA: 4150 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 964053 Total methylated C's in CpG context: 22665 Total methylated C's in CHG context: 24412 Total methylated C's in CHH context: 39988 Total methylated C's in Unknown context: 435 Total unmethylated C's in CpG context: 220063 Total unmethylated C's in CHG context: 238970 Total unmethylated C's in CHH context: 417955 Total unmethylated C's in Unknown context: 2325 C methylated in CpG context: 9.3% C methylated in CHG context: 9.3% C methylated in CHH context: 8.7% C methylated in unknown context (CN or CHN): 15.8% Bismark completed in 0d 0h 55m 46s