Bismark report for: /Volumes/web/seashell/bu-serine-wd/18-04-07/zr2096_3_s1_R1.fastq.gz and /Volumes/web/seashell/bu-serine-wd/18-04-07/zr2096_3_s1_R2.fastq.gz (version: v0.20.0) Bismark was run with Bowtie 2 against the bisulfite genome of /Volumes/web/metacarcinus/Cvirginica/GENOMES/v300/Bismark_genome/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --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: 100000 Number of paired-end alignments with a unique best hit: 51869 Mapping efficiency: 51.9% Sequence pairs with no alignments under any condition: 31536 Sequence pairs did not map uniquely: 16595 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: 13049 ((converted) top strand) GA/CT/CT: 12928 (complementary to (converted) top strand) GA/CT/GA: 12824 (complementary to (converted) bottom strand) CT/GA/GA: 13068 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1846054 Total methylated C's in CpG context: 205232 Total methylated C's in CHG context: 13018 Total methylated C's in CHH context: 43410 Total methylated C's in Unknown context: 5954 Total unmethylated C's in CpG context: 64206 Total unmethylated C's in CHG context: 410867 Total unmethylated C's in CHH context: 1109321 Total unmethylated C's in Unknown context: 26408 C methylated in CpG context: 76.2% C methylated in CHG context: 3.1% C methylated in CHH context: 3.8% C methylated in unknown context (CN or CHN): 18.4% Bismark completed in 0d 0h 2m 21s