Bismark report for: ../../data/raw-wgbs/93M_1.fastq.gz and ../../data/raw-wgbs/93M_2.fastq.gz (version: v0.24.2) Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/ with the specified options: -q --score-min L,0,-0.6 -p 30 --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: 4804 Mapping efficiency: 48.0% Sequence pairs with no alignments under any condition: 3993 Sequence pairs did not map uniquely: 1203 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: 2422 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 2 (complementary to (converted) bottom strand) CT/GA/GA: 2380 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 226753 Total methylated C's in CpG context: 3429 Total methylated C's in CHG context: 1098 Total methylated C's in CHH context: 5160 Total methylated C's in Unknown context: 271 Total unmethylated C's in CpG context: 23082 Total unmethylated C's in CHG context: 35564 Total unmethylated C's in CHH context: 158420 Total unmethylated C's in Unknown context: 964 C methylated in CpG context: 12.9% C methylated in CHG context: 3.0% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 21.9% Bismark completed in 0d 0h 0m 20s