Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF03-EM03-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF03-EM03-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: 132787654 Number of paired-end alignments with a unique best hit: 24296257 Mapping efficiency: 18.3% Sequence pairs with no alignments under any condition: 94202406 Sequence pairs did not map uniquely: 14288991 Sequence pairs which were discarded because genomic sequence could not be extracted: 6 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6744796 ((converted) top strand) GA/CT/CT: 5426945 (complementary to (converted) top strand) GA/CT/GA: 5402692 (complementary to (converted) bottom strand) CT/GA/GA: 6721818 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 511101837 Total methylated C's in CpG context: 12712115 Total methylated C's in CHG context: 3117783 Total methylated C's in CHH context: 26175201 Total methylated C's in Unknown context: 660360 Total unmethylated C's in CpG context: 46597944 Total unmethylated C's in CHG context: 86336289 Total unmethylated C's in CHH context: 336162505 Total unmethylated C's in Unknown context: 3082294 C methylated in CpG context: 21.4% C methylated in CHG context: 3.5% C methylated in CHH context: 7.2% C methylated in unknown context (CN or CHN): 17.6% Bismark completed in 0d 4h 49m 9s