Bismark report for: /gscratch/srlab/sr320/data/cg-big/0501_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/0501_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: 59640 Mapping efficiency: 59.6% Sequence pairs with no alignments under any condition: 30009 Sequence pairs did not map uniquely: 10351 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: 29836 ((converted) top strand) GA/CT/CT: 13 (complementary to (converted) top strand) GA/CT/GA: 14 (complementary to (converted) bottom strand) CT/GA/GA: 29777 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2510127 Total methylated C's in CpG context: 39770 Total methylated C's in CHG context: 3532 Total methylated C's in CHH context: 16591 Total methylated C's in Unknown context: 262 Total unmethylated C's in CpG context: 262307 Total unmethylated C's in CHG context: 406581 Total unmethylated C's in CHH context: 1781346 Total unmethylated C's in Unknown context: 7688 C methylated in CpG context: 13.2% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 3.3% Bismark completed in 0d 0h 0m 56s