Bismark report for: /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R2.fq.gz (version: v0.22.3) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ 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: 100000 Number of paired-end alignments with a unique best hit: 60858 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 22549 Sequence pairs did not map uniquely: 16593 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15316 ((converted) top strand) GA/CT/CT: 15202 (complementary to (converted) top strand) GA/CT/GA: 15237 (complementary to (converted) bottom strand) CT/GA/GA: 15102 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2144468 Total methylated C's in CpG context: 29213 Total methylated C's in CHG context: 1771 Total methylated C's in CHH context: 7827 Total methylated C's in Unknown context: 73 Total unmethylated C's in CpG context: 248391 Total unmethylated C's in CHG context: 372784 Total unmethylated C's in CHH context: 1484482 Total unmethylated C's in Unknown context: 5270 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 49s