Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF05-EM06-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF05-EM06-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: 62575164 Number of paired-end alignments with a unique best hit: 21714872 Mapping efficiency: 34.7% Sequence pairs with no alignments under any condition: 32866900 Sequence pairs did not map uniquely: 7993392 Sequence pairs which were discarded because genomic sequence could not be extracted: 8 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5154322 ((converted) top strand) GA/CT/CT: 5691891 (complementary to (converted) top strand) GA/CT/GA: 5710450 (complementary to (converted) bottom strand) CT/GA/GA: 5158201 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 830731865 Total methylated C's in CpG context: 22400465 Total methylated C's in CHG context: 6818064 Total methylated C's in CHH context: 29976832 Total methylated C's in Unknown context: 454341 Total unmethylated C's in CpG context: 90547001 Total unmethylated C's in CHG context: 153083789 Total unmethylated C's in CHH context: 527905714 Total unmethylated C's in Unknown context: 3354289 C methylated in CpG context: 19.8% C methylated in CHG context: 4.3% C methylated in CHH context: 5.4% C methylated in unknown context (CN or CHN): 11.9% Bismark completed in 1d 3h 37m 19s