Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_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/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 '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) Final Alignment report ====================== Sequence pairs analysed in total: 27792315 Number of paired-end alignments with a unique best hit: 12229034 Mapping efficiency: 44.0% Sequence pairs with no alignments under any condition: 12912342 Sequence pairs did not map uniquely: 2650939 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 6066303 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6162730 ((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: 371098859 Total methylated C's in CpG context: 12526554 Total methylated C's in CHG context: 1883224 Total methylated C's in CHH context: 2923602 Total methylated C's in Unknown context: 54090 Total unmethylated C's in CpG context: 39735089 Total unmethylated C's in CHG context: 76137777 Total unmethylated C's in CHH context: 237892613 Total unmethylated C's in Unknown context: 810936 C methylated in CpG context: 24.0% C methylated in CHG context: 2.4% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 6.3% Bismark completed in 0d 1h 38m 18s