Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-227_S35_L004_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: 44661 Mapping efficiency: 44.7% Sequence pairs with no alignments under any condition: 43895 Sequence pairs did not map uniquely: 11444 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: 20749 ((converted) top strand) GA/CT/CT: 1239 (complementary to (converted) top strand) GA/CT/GA: 1231 (complementary to (converted) bottom strand) CT/GA/GA: 21442 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1329207 Total methylated C's in CpG context: 53928 Total methylated C's in CHG context: 7314 Total methylated C's in CHH context: 51209 Total methylated C's in Unknown context: 647 Total unmethylated C's in CpG context: 126519 Total unmethylated C's in CHG context: 269265 Total unmethylated C's in CHH context: 820972 Total unmethylated C's in Unknown context: 2980 C methylated in CpG context: 29.9% C methylated in CHG context: 2.6% C methylated in CHH context: 5.9% C methylated in unknown context (CN or CHN): 17.8% Bismark completed in 4d 6h 1m 40s