Bismark report for: /gscratch/scrubbed/sr320/froger-trim/Meth5.fastp-trim.202003051832_R1_001.fastq.gz and /gscratch/scrubbed/sr320/froger-trim/Meth5.fastp-trim.202003051832_R2_001.fastq.gz (version: v0.21.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Pdam_Genome/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB) Final Alignment report ====================== Sequence pairs analysed in total: 10000 Number of paired-end alignments with a unique best hit: 3458 Mapping efficiency: 34.6% Sequence pairs with no alignments under any condition: 6092 Sequence pairs did not map uniquely: 450 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: 868 ((converted) top strand) GA/CT/CT: 903 (complementary to (converted) top strand) GA/CT/GA: 873 (complementary to (converted) bottom strand) CT/GA/GA: 814 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 150425 Total methylated C's in CpG context: 3961 Total methylated C's in CHG context: 228 Total methylated C's in CHH context: 526 Total methylated C's in Unknown context: 3 Total unmethylated C's in CpG context: 28481 Total unmethylated C's in CHG context: 29469 Total unmethylated C's in CHH context: 87760 Total unmethylated C's in Unknown context: 121 C methylated in CpG context: 12.2% C methylated in CHG context: 0.8% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 2.4% Bismark completed in 0d 0h 0m 17s