Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-152_S3_L002_R2_001_val_2.fq.gz (version: v0.21.0_dev) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/geoduck/v074/ with the specified options: -q --score-min L,0,-0.6 -p 28 --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: 100000 Number of paired-end alignments with a unique best hit: 40472 Mapping efficiency: 40.5% Sequence pairs with no alignments under any condition: 50750 Sequence pairs did not map uniquely: 8778 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: 19323 ((converted) top strand) GA/CT/CT: 781 (complementary to (converted) top strand) GA/CT/GA: 792 (complementary to (converted) bottom strand) CT/GA/GA: 19576 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1258945 Total methylated C's in CpG context: 49975 Total methylated C's in CHG context: 6498 Total methylated C's in CHH context: 45498 Total methylated C's in Unknown context: 527 Total unmethylated C's in CpG context: 118253 Total unmethylated C's in CHG context: 253146 Total unmethylated C's in CHH context: 785575 Total unmethylated C's in Unknown context: 2825 C methylated in CpG context: 29.7% C methylated in CHG context: 2.5% C methylated in CHH context: 5.5% C methylated in unknown context (CN or CHN): 15.7% Bismark completed in 1d 8h 53m 21s