Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF08-CM05-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF08-CM05-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 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: 63057346 Number of paired-end alignments with a unique best hit: 1698854 Mapping efficiency: 2.7% Sequence pairs with no alignments under any condition: 60469188 Sequence pairs did not map uniquely: 889304 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 435646 ((converted) top strand) GA/CT/CT: 412268 (complementary to (converted) top strand) GA/CT/GA: 413487 (complementary to (converted) bottom strand) CT/GA/GA: 437453 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 53131425 Total methylated C's in CpG context: 968715 Total methylated C's in CHG context: 154154 Total methylated C's in CHH context: 2898885 Total methylated C's in Unknown context: 86455 Total unmethylated C's in CpG context: 5085353 Total unmethylated C's in CHG context: 8738717 Total unmethylated C's in CHH context: 35285601 Total unmethylated C's in Unknown context: 270113 C methylated in CpG context: 16.0% C methylated in CHG context: 1.7% C methylated in CHH context: 7.6% C methylated in unknown context (CN or CHN): 24.2% Bismark completed in 0d 2h 53m 53s