Bismark report for: /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF01-EM01-Zygote_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF01-EM01-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: 47718725 Number of paired-end alignments with a unique best hit: 11837827 Mapping efficiency: 24.8% Sequence pairs with no alignments under any condition: 30005679 Sequence pairs did not map uniquely: 5875219 Sequence pairs which were discarded because genomic sequence could not be extracted: 3 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3036089 ((converted) top strand) GA/CT/CT: 2904525 (complementary to (converted) top strand) GA/CT/GA: 2881668 (complementary to (converted) bottom strand) CT/GA/GA: 3015542 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 315419211 Total methylated C's in CpG context: 10028002 Total methylated C's in CHG context: 2595448 Total methylated C's in CHH context: 15258811 Total methylated C's in Unknown context: 341029 Total unmethylated C's in CpG context: 30898045 Total unmethylated C's in CHG context: 58865061 Total unmethylated C's in CHH context: 197773844 Total unmethylated C's in Unknown context: 1525870 C methylated in CpG context: 24.5% C methylated in CHG context: 4.2% C methylated in CHH context: 7.2% C methylated in unknown context (CN or CHN): 18.3% Bismark completed in 0d 2h 9m 17s