Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF01-CM01-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF01-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 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: 32105151 Number of paired-end alignments with a unique best hit: 4636366 Mapping efficiency: 14.4% Sequence pairs with no alignments under any condition: 24877118 Sequence pairs did not map uniquely: 2591667 Sequence pairs which were discarded because genomic sequence could not be extracted: 10 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 1252794 ((converted) top strand) GA/CT/CT: 1075456 (complementary to (converted) top strand) GA/CT/GA: 1067723 (complementary to (converted) bottom strand) CT/GA/GA: 1240383 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 104445771 Total methylated C's in CpG context: 2042686 Total methylated C's in CHG context: 232168 Total methylated C's in CHH context: 3647880 Total methylated C's in Unknown context: 104660 Total unmethylated C's in CpG context: 9965003 Total unmethylated C's in CHG context: 17465052 Total unmethylated C's in CHH context: 71092982 Total unmethylated C's in Unknown context: 689325 C methylated in CpG context: 17.0% C methylated in CHG context: 1.3% C methylated in CHH context: 4.9% C methylated in unknown context (CN or CHN): 13.2% Bismark completed in 0d 6h 50m 55s