Bismark report for: /gscratch/scrubbed/sr320/froger-trim/Meth15.fastp-trim.202003050057_R1_001.fastq.gz and /gscratch/scrubbed/sr320/froger-trim/Meth15.fastp-trim.202003050057_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: 43 Mapping efficiency: 0.4% Sequence pairs with no alignments under any condition: 9916 Sequence pairs did not map uniquely: 41 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: 8 ((converted) top strand) GA/CT/CT: 11 (complementary to (converted) top strand) GA/CT/GA: 12 (complementary to (converted) bottom strand) CT/GA/GA: 12 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 812 Total methylated C's in CpG context: 50 Total methylated C's in CHG context: 3 Total methylated C's in CHH context: 79 Total methylated C's in Unknown context: 0 Total unmethylated C's in CpG context: 95 Total unmethylated C's in CHG context: 174 Total unmethylated C's in CHH context: 411 Total unmethylated C's in Unknown context: 0 C methylated in CpG context: 34.5% C methylated in CHG context: 1.7% C methylated in CHH context: 16.1% Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0 Bismark completed in 0d 0h 0m 15s