Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF04-EM05-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF04-EM05-Larvae_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/Cvirg-genome/ with the specified options: -q --score-min L,0,-0.6 -p 8 --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: 45628766 Number of paired-end alignments with a unique best hit: 16508157 Mapping efficiency: 36.2% Sequence pairs with no alignments under any condition: 21474728 Sequence pairs did not map uniquely: 7645881 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3903278 ((converted) top strand) GA/CT/CT: 4347635 (complementary to (converted) top strand) GA/CT/GA: 4353913 (complementary to (converted) bottom strand) CT/GA/GA: 3903326 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 576961869 Total methylated C's in CpG context: 15192000 Total methylated C's in CHG context: 1474807 Total methylated C's in CHH context: 7395303 Total methylated C's in Unknown context: 261520 Total unmethylated C's in CpG context: 69576219 Total unmethylated C's in CHG context: 117554488 Total unmethylated C's in CHH context: 365769052 Total unmethylated C's in Unknown context: 2415126 C methylated in CpG context: 17.9% C methylated in CHG context: 1.2% C methylated in CHH context: 2.0% C methylated in unknown context (CN or CHN): 9.8% Bismark completed in 0d 19h 26m 19s