Bismark report for: /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/cat_lanes/Sealice_F2_S22_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/cat_lanes/Sealice_F2_S22_R2_001_val_2.fq.gz (version: v0.22.3) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Caligus/GENOMES/ with the specified options: -q --score-min L,0,-0.6 -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: 163179589 Number of paired-end alignments with a unique best hit: 34864893 Mapping efficiency: 21.4% Sequence pairs with no alignments under any condition: 96900506 Sequence pairs did not map uniquely: 31414190 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: 8811566 ((converted) top strand) GA/CT/CT: 8734683 (complementary to (converted) top strand) GA/CT/GA: 8632124 (complementary to (converted) bottom strand) CT/GA/GA: 8686520 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1312764401 Total methylated C's in CpG context: 2228643 Total methylated C's in CHG context: 1681346 Total methylated C's in CHH context: 13086203 Total methylated C's in Unknown context: 926494 Total unmethylated C's in CpG context: 209534428 Total unmethylated C's in CHG context: 214906295 Total unmethylated C's in CHH context: 871327486 Total unmethylated C's in Unknown context: 11603924 C methylated in CpG context: 1.1% C methylated in CHG context: 0.8% C methylated in CHH context: 1.5% C methylated in unknown context (CN or CHN): 7.4% Bismark completed in 0d 5h 26m 8s