Bismark report for: /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R1_001.fastq.gz and /gscratch/srlab/sr320/data/caligus/reads/raw/Sealice_F2_S22_L001_R2_001.fastq.gz (version: v0.21.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/caligus/genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) Final Alignment report ====================== Sequence pairs analysed in total: 82177525 Number of paired-end alignments with a unique best hit: 4815592 Mapping efficiency: 5.9% Sequence pairs with no alignments under any condition: 74812200 Sequence pairs did not map uniquely: 2549733 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: 2416982 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 2398610 ((converted) bottom strand) Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 Final Cytosine Methylation Report ================================= Total number of C's analysed: 269443330 Total methylated C's in CpG context: 1442407 Total methylated C's in CHG context: 1137082 Total methylated C's in CHH context: 5281990 Total methylated C's in Unknown context: 1010601 Total unmethylated C's in CpG context: 42169766 Total unmethylated C's in CHG context: 43933031 Total unmethylated C's in CHH context: 175479054 Total unmethylated C's in Unknown context: 2663577 C methylated in CpG context: 3.3% C methylated in CHG context: 2.5% C methylated in CHH context: 2.9% C methylated in unknown context (CN or CHN): 27.5% Bismark completed in 0d 4h 11m 5s