Bismark report for: /gscratch/scrubbed/sr320/froger-trim/Meth4.fastp-trim.202003055221_R1_001.fastq.gz and /gscratch/scrubbed/sr320/froger-trim/Meth4.fastp-trim.202003055221_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: 3317 Mapping efficiency: 33.2% Sequence pairs with no alignments under any condition: 6265 Sequence pairs did not map uniquely: 418 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: 827 ((converted) top strand) GA/CT/CT: 841 (complementary to (converted) top strand) GA/CT/GA: 823 (complementary to (converted) bottom strand) CT/GA/GA: 826 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 142861 Total methylated C's in CpG context: 3879 Total methylated C's in CHG context: 313 Total methylated C's in CHH context: 660 Total methylated C's in Unknown context: 2 Total unmethylated C's in CpG context: 27595 Total unmethylated C's in CHG context: 28429 Total unmethylated C's in CHH context: 81985 Total unmethylated C's in Unknown context: 126 C methylated in CpG context: 12.3% C methylated in CHG context: 1.1% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 18s