Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-194_S23_L003_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: 43422 Mapping efficiency: 43.4% Sequence pairs with no alignments under any condition: 47401 Sequence pairs did not map uniquely: 9177 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: 20524 ((converted) top strand) GA/CT/CT: 850 (complementary to (converted) top strand) GA/CT/GA: 830 (complementary to (converted) bottom strand) CT/GA/GA: 21218 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1371773 Total methylated C's in CpG context: 56309 Total methylated C's in CHG context: 6811 Total methylated C's in CHH context: 50466 Total methylated C's in Unknown context: 530 Total unmethylated C's in CpG context: 128701 Total unmethylated C's in CHG context: 279332 Total unmethylated C's in CHH context: 850154 Total unmethylated C's in Unknown context: 2960 C methylated in CpG context: 30.4% C methylated in CHG context: 2.4% C methylated in CHH context: 5.6% C methylated in unknown context (CN or CHN): 15.2% Bismark completed in 3d 4h 3m 45s