Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF01-CM02-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/CF01-CM02-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: 70708148 Number of paired-end alignments with a unique best hit: 24971340 Mapping efficiency: 35.3% Sequence pairs with no alignments under any condition: 32368850 Sequence pairs did not map uniquely: 13367958 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: 6075606 ((converted) top strand) GA/CT/CT: 6411238 (complementary to (converted) top strand) GA/CT/GA: 6406104 (complementary to (converted) bottom strand) CT/GA/GA: 6078385 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 761919570 Total methylated C's in CpG context: 21632951 Total methylated C's in CHG context: 2849382 Total methylated C's in CHH context: 15683163 Total methylated C's in Unknown context: 457724 Total unmethylated C's in CpG context: 93811696 Total unmethylated C's in CHG context: 157562798 Total unmethylated C's in CHH context: 470379580 Total unmethylated C's in Unknown context: 3211503 C methylated in CpG context: 18.7% C methylated in CHG context: 1.8% C methylated in CHH context: 3.2% C methylated in unknown context (CN or CHN): 12.5% Bismark completed in 0d 4h 7m 23s