Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-215_S31_L004_R2_001_val_2.fq.gz (version: v0.21.0_dev) 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,-0.6 -p 28 --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: 100000 Number of paired-end alignments with a unique best hit: 43486 Mapping efficiency: 43.5% Sequence pairs with no alignments under any condition: 43666 Sequence pairs did not map uniquely: 12848 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 20177 ((converted) top strand) GA/CT/CT: 1219 (complementary to (converted) top strand) GA/CT/GA: 1270 (complementary to (converted) bottom strand) CT/GA/GA: 20820 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1267261 Total methylated C's in CpG context: 55024 Total methylated C's in CHG context: 7467 Total methylated C's in CHH context: 51124 Total methylated C's in Unknown context: 726 Total unmethylated C's in CpG context: 119794 Total unmethylated C's in CHG context: 257247 Total unmethylated C's in CHH context: 776605 Total unmethylated C's in Unknown context: 2910 C methylated in CpG context: 31.5% C methylated in CHG context: 2.8% C methylated in CHH context: 6.2% C methylated in unknown context (CN or CHN): 20.0% Bismark completed in 3d 21h 0m 18s