Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF04-EM04-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF04-EM04-Zygote_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: 70141415 Number of paired-end alignments with a unique best hit: 9554896 Mapping efficiency: 13.6% Sequence pairs with no alignments under any condition: 54144932 Sequence pairs did not map uniquely: 6441587 Sequence pairs which were discarded because genomic sequence could not be extracted: 24 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2369042 ((converted) top strand) GA/CT/CT: 2422982 (complementary to (converted) top strand) GA/CT/GA: 2410386 (complementary to (converted) bottom strand) CT/GA/GA: 2352462 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 179687816 Total methylated C's in CpG context: 3894966 Total methylated C's in CHG context: 1072401 Total methylated C's in CHH context: 8124397 Total methylated C's in Unknown context: 288360 Total unmethylated C's in CpG context: 18819198 Total unmethylated C's in CHG context: 30837097 Total unmethylated C's in CHH context: 116939757 Total unmethylated C's in Unknown context: 1597788 C methylated in CpG context: 17.1% C methylated in CHG context: 3.4% C methylated in CHH context: 6.5% C methylated in unknown context (CN or CHN): 15.3% Bismark completed in 0d 14h 24m 48s