Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF03-CM04-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF03-CM04-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: 57667284 Number of paired-end alignments with a unique best hit: 25131000 Mapping efficiency: 43.6% Sequence pairs with no alignments under any condition: 19755662 Sequence pairs did not map uniquely: 12780622 Sequence pairs which were discarded because genomic sequence could not be extracted: 13 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6016951 ((converted) top strand) GA/CT/CT: 6529185 (complementary to (converted) top strand) GA/CT/GA: 6558200 (complementary to (converted) bottom strand) CT/GA/GA: 6026651 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 849535844 Total methylated C's in CpG context: 22926977 Total methylated C's in CHG context: 2029014 Total methylated C's in CHH context: 10201931 Total methylated C's in Unknown context: 286774 Total unmethylated C's in CpG context: 97913175 Total unmethylated C's in CHG context: 171554242 Total unmethylated C's in CHH context: 544910505 Total unmethylated C's in Unknown context: 3165460 C methylated in CpG context: 19.0% C methylated in CHG context: 1.2% C methylated in CHH context: 1.8% C methylated in unknown context (CN or CHN): 8.3% Bismark completed in 1d 3h 36m 19s