Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-154_S5_L002_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: 25226760 Number of paired-end alignments with a unique best hit: 9405544 Mapping efficiency: 37.3% Sequence pairs with no alignments under any condition: 13904236 Sequence pairs did not map uniquely: 1916980 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: 4637602 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4767942 ((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: 285373397 Total methylated C's in CpG context: 11306006 Total methylated C's in CHG context: 1298778 Total methylated C's in CHH context: 3449101 Total methylated C's in Unknown context: 62682 Total unmethylated C's in CpG context: 28242299 Total unmethylated C's in CHG context: 60128621 Total unmethylated C's in CHH context: 180948592 Total unmethylated C's in Unknown context: 625876 C methylated in CpG context: 28.6% C methylated in CHG context: 2.1% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 9.1% Bismark completed in 0d 1h 20m 15s