Bismark report for: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R1_001.fastp-trim.20220827.fq.gz and /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF05-CM02-Larvae_R2_001.fastp-trim.20220827.fq.gz (version: v0.24.0) Bismark was run with Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300/ with the specified options: -q --score-min L,0,-0.6 -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: 164974181 Number of paired-end alignments with a unique best hit: 58761317 Mapping efficiency: 35.6% Sequence pairs with no alignments under any condition: 82780086 Sequence pairs did not map uniquely: 23432778 Sequence pairs which were discarded because genomic sequence could not be extracted: 82 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 13789582 ((converted) top strand) GA/CT/CT: 15541468 (complementary to (converted) top strand) GA/CT/GA: 15579544 (complementary to (converted) bottom strand) CT/GA/GA: 13850641 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2337459015 Total methylated C's in CpG context: 61688308 Total methylated C's in CHG context: 8318037 Total methylated C's in CHH context: 34366183 Total methylated C's in Unknown context: 2277768 Total unmethylated C's in CpG context: 292984115 Total unmethylated C's in CHG context: 498126240 Total unmethylated C's in CHH context: 1441976132 Total unmethylated C's in Unknown context: 10951237 C methylated in CpG context: 17.4% C methylated in CHG context: 1.6% C methylated in CHH context: 2.3% C methylated in unknown context (CN or CHN): 17.2% Bismark completed in 0d 6h 51m 39s