Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-42_S39_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: 29623269 Number of paired-end alignments with a unique best hit: 13173399 Mapping efficiency: 44.5% Sequence pairs with no alignments under any condition: 13088150 Sequence pairs did not map uniquely: 3361720 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: 6518218 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 6655181 ((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: 371864315 Total methylated C's in CpG context: 17401813 Total methylated C's in CHG context: 2029825 Total methylated C's in CHH context: 4531660 Total methylated C's in Unknown context: 68790 Total unmethylated C's in CpG context: 35533244 Total unmethylated C's in CHG context: 78200824 Total unmethylated C's in CHH context: 234166949 Total unmethylated C's in Unknown context: 781521 C methylated in CpG context: 32.9% C methylated in CHG context: 2.5% C methylated in CHH context: 1.9% C methylated in unknown context (CN or CHN): 8.1% Bismark completed in 0d 1h 17m 56s