Bismark report for: /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_5_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: 61435 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 22294 Sequence pairs did not map uniquely: 16271 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: 15396 ((converted) top strand) GA/CT/CT: 15226 (complementary to (converted) top strand) GA/CT/GA: 15288 (complementary to (converted) bottom strand) CT/GA/GA: 15525 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2137438 Total methylated C's in CpG context: 31070 Total methylated C's in CHG context: 1884 Total methylated C's in CHH context: 8105 Total methylated C's in Unknown context: 60 Total unmethylated C's in CpG context: 244356 Total unmethylated C's in CHG context: 371466 Total unmethylated C's in CHH context: 1480557 Total unmethylated C's in Unknown context: 5408 C methylated in CpG context: 11.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 50s