Bismark report for: ../../data/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz and ../../data/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz (version: v0.24.2) Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/ceasmallr/data/genome/ with the specified options: -q --score-min L,0,-0.6 -p 8 --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: 1284 Mapping efficiency: 12.8% Sequence pairs with no alignments under any condition: 8163 Sequence pairs did not map uniquely: 553 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: 373 ((converted) top strand) GA/CT/CT: 298 (complementary to (converted) top strand) GA/CT/GA: 291 (complementary to (converted) bottom strand) CT/GA/GA: 322 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 36160 Total methylated C's in CpG context: 803 Total methylated C's in CHG context: 165 Total methylated C's in CHH context: 666 Total methylated C's in Unknown context: 73 Total unmethylated C's in CpG context: 4073 Total unmethylated C's in CHG context: 6324 Total unmethylated C's in CHH context: 24129 Total unmethylated C's in Unknown context: 247 C methylated in CpG context: 16.5% C methylated in CHG context: 2.5% C methylated in CHH context: 2.7% C methylated in Unknown context (CN or CHN): 22.8% Bismark completed in 0d 0h 0m 14s