Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank2-025-026_R1_001.fastq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank2-025-026_R2_001.fastq.gz (version: v0.19.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Pgenr/Pgenr_070_10K/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --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: 66223383 Number of paired-end alignments with a unique best hit: 44278491 Mapping efficiency: 66.9% Sequence pairs with no alignments under any condition: 16030925 Sequence pairs did not map uniquely: 5913967 Sequence pairs which were discarded because genomic sequence could not be extracted: 56477 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 22102670 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 22119344 ((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: 2079183930 Total methylated C's in CpG context: 47472216 Total methylated C's in CHG context: 12595147 Total methylated C's in CHH context: 50893372 Total methylated C's in Unknown context: 2978390 Total unmethylated C's in CpG context: 198031144 Total unmethylated C's in CHG context: 360551956 Total unmethylated C's in CHH context: 1409640095 Total unmethylated C's in Unknown context: 14288075 C methylated in CpG context: 19.3% C methylated in CHG context: 3.4% C methylated in CHH context: 3.5% C methylated in unknown context (CN or CHN): 17.2% Bismark completed in 0d 23h 44m 31s