Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Pact_trim/Meth6_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Pact_trim/Meth6_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/froger/Pact_Genome/ 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: 140382105 Number of paired-end alignments with a unique best hit: 83397559 Mapping efficiency: 59.4% Sequence pairs with no alignments under any condition: 41621882 Sequence pairs did not map uniquely: 15362664 Sequence pairs which were discarded because genomic sequence could not be extracted: 894484 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 19831080 ((converted) top strand) GA/CT/CT: 21707893 (complementary to (converted) top strand) GA/CT/GA: 21489288 (complementary to (converted) bottom strand) CT/GA/GA: 19474814 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 3767163573 Total methylated C's in CpG context: 42113055 Total methylated C's in CHG context: 6710796 Total methylated C's in CHH context: 20938786 Total methylated C's in Unknown context: 380161 Total unmethylated C's in CpG context: 781441274 Total unmethylated C's in CHG context: 737267371 Total unmethylated C's in CHH context: 2178692291 Total unmethylated C's in Unknown context: 6724335 C methylated in CpG context: 5.1% C methylated in CHG context: 0.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 5.4% Bismark completed in 0d 13h 14m 51s