Bismark report for: /gscratch/scrubbed/yaamini/data/Gigas-WGBS/2019-09-03-Trimmed-Files/YRVL_R1_001.fastq.gz and /gscratch/scrubbed/yaamini/data/Gigas-WGBS/2019-09-03-Trimmed-Files/YRVL_R2_001.fastq.gz (version: v0.21.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/yaamini/data/Gigas-WGBS/2019-09-03-Bismark-Inputs/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ with the specified options: -q --score-min L,0,-0.9 -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: 66590575 Number of paired-end alignments with a unique best hit: 42554384 Mapping efficiency: 63.9% Sequence pairs with no alignments under any condition: 19593685 Sequence pairs did not map uniquely: 4442506 Sequence pairs which were discarded because genomic sequence could not be extracted: 15181 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 21265268 ((converted) top strand) GA/CT/CT: 12105 (complementary to (converted) top strand) GA/CT/GA: 13209 (complementary to (converted) bottom strand) CT/GA/GA: 21248621 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1975323986 Total methylated C's in CpG context: 36708077 Total methylated C's in CHG context: 12605227 Total methylated C's in CHH context: 59188038 Total methylated C's in Unknown context: 2509847 Total unmethylated C's in CpG context: 203868749 Total unmethylated C's in CHG context: 314647529 Total unmethylated C's in CHH context: 1348306366 Total unmethylated C's in Unknown context: 12087334 C methylated in CpG context: 15.3% C methylated in CHG context: 3.9% C methylated in CHH context: 4.2% C methylated in unknown context (CN or CHN): 17.2% Bismark completed in 0d 7h 37m 10s