Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-193_S22_L003_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/v074/ 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: 26770469 Number of paired-end alignments with a unique best hit: 10697352 Mapping efficiency: 40.0% Sequence pairs with no alignments under any condition: 13242455 Sequence pairs did not map uniquely: 2830662 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: 5278754 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 5418598 ((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: 301211333 Total methylated C's in CpG context: 12254387 Total methylated C's in CHG context: 1506836 Total methylated C's in CHH context: 3959201 Total methylated C's in Unknown context: 62246 Total unmethylated C's in CpG context: 30734018 Total unmethylated C's in CHG context: 63666955 Total unmethylated C's in CHH context: 189089936 Total unmethylated C's in Unknown context: 644527 C methylated in CpG context: 28.5% C methylated in CHG context: 2.3% C methylated in CHH context: 2.1% C methylated in unknown context (CN or CHN): 8.8% Bismark completed in 0d 1h 38m 44s