Bismark report for: /gscratch/scrubbed/strigg/analyses/20200930/Tank3-15-16_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200930/Tank3-15-16_R2_001_val_2.fq.gz (version: v0.22.3) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v01/ 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: 49288195 Number of paired-end alignments with a unique best hit: 23549660 Mapping efficiency: 47.8% Sequence pairs with no alignments under any condition: 23448875 Sequence pairs did not map uniquely: 2289660 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: 11728351 ((converted) top strand) GA/CT/CT: 53358 (complementary to (converted) top strand) GA/CT/GA: 53028 (complementary to (converted) bottom strand) CT/GA/GA: 11714920 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 965270762 Total methylated C's in CpG context: 21756693 Total methylated C's in CHG context: 2018964 Total methylated C's in CHH context: 12826491 Total methylated C's in Unknown context: 118670 Total unmethylated C's in CpG context: 91211097 Total unmethylated C's in CHG context: 167755459 Total unmethylated C's in CHH context: 669702058 Total unmethylated C's in Unknown context: 2142254 C methylated in CpG context: 19.3% C methylated in CHG context: 1.2% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 5.2% Bismark completed in 0d 3h 25m 7s