Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF06-CM01-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF06-CM01-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 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: 82389335 Number of paired-end alignments with a unique best hit: 21391013 Mapping efficiency: 26.0% Sequence pairs with no alignments under any condition: 49144786 Sequence pairs did not map uniquely: 11853536 Sequence pairs which were discarded because genomic sequence could not be extracted: 7 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 5828753 ((converted) top strand) GA/CT/CT: 4879701 (complementary to (converted) top strand) GA/CT/GA: 4871977 (complementary to (converted) bottom strand) CT/GA/GA: 5810575 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 486705678 Total methylated C's in CpG context: 13309555 Total methylated C's in CHG context: 2668182 Total methylated C's in CHH context: 20162803 Total methylated C's in Unknown context: 485728 Total unmethylated C's in CpG context: 47870691 Total unmethylated C's in CHG context: 87089171 Total unmethylated C's in CHH context: 315605276 Total unmethylated C's in Unknown context: 2841411 C methylated in CpG context: 21.8% C methylated in CHG context: 3.0% C methylated in CHH context: 6.0% C methylated in unknown context (CN or CHN): 14.6% Bismark completed in 0d 3h 43m 19s