Bismark report for: /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R2_001_val_2.fq.gz (version: v0.19.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-1.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --maxins 500 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) Final Alignment report ====================== Sequence pairs analysed in total: 16541499 Number of paired-end alignments with a unique best hit: 7025382 Mapping efficiency: 42.5% Sequence pairs with no alignments under any condition: 8039389 Sequence pairs did not map uniquely: 1476728 Sequence pairs which were discarded because genomic sequence could not be extracted: 20 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3423867 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 3601495 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 203655615 Total methylated C's in CpG context: 7398519 Total methylated C's in CHG context: 1161571 Total methylated C's in CHH context: 4560293 Total methylated C's in Unknown context: 178365 Total unmethylated C's in CpG context: 22754525 Total unmethylated C's in CHG context: 43791734 Total unmethylated C's in CHH context: 123988973 Total unmethylated C's in Unknown context: 1416101 C methylated in CpG context: 24.5% C methylated in CHG context: 2.6% C methylated in CHH context: 3.5% C methylated in unknown context (CN or CHN): 11.2% Bismark completed in 0d 1h 10m 3s