Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_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: 28731808 Number of paired-end alignments with a unique best hit: 12720631 Mapping efficiency: 44.3% Sequence pairs with no alignments under any condition: 13210078 Sequence pairs did not map uniquely: 2801099 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: 6307893 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6412737 ((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: 379885177 Total methylated C's in CpG context: 14174074 Total methylated C's in CHG context: 2097825 Total methylated C's in CHH context: 3204273 Total methylated C's in Unknown context: 64166 Total unmethylated C's in CpG context: 39497431 Total unmethylated C's in CHG context: 77915331 Total unmethylated C's in CHH context: 242996243 Total unmethylated C's in Unknown context: 785379 C methylated in CpG context: 26.4% C methylated in CHG context: 2.6% C methylated in CHH context: 1.3% C methylated in unknown context (CN or CHN): 7.6% Bismark completed in 0d 1h 43m 26s