Bismark report for: /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_s1_R2.fastq.gz (version: v0.19.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ with the specified options: -q --score-min L,0,-1.2 --ignore-quals --no-mixed --no-discordant --dovetail --minins 100 --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: 29761837 Number of paired-end alignments with a unique best hit: 9031924 Mapping efficiency: 30.3% Sequence pairs with no alignments under any condition: 18352667 Sequence pairs did not map uniquely: 2377246 Sequence pairs which were discarded because genomic sequence could not be extracted: 5 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2310227 ((converted) top strand) GA/CT/CT: 2208932 (complementary to (converted) top strand) GA/CT/GA: 2211243 (complementary to (converted) bottom strand) CT/GA/GA: 2301517 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 319685131 Total methylated C's in CpG context: 25081844 Total methylated C's in CHG context: 2220090 Total methylated C's in CHH context: 9298556 Total methylated C's in Unknown context: 1029157 Total unmethylated C's in CpG context: 13629344 Total unmethylated C's in CHG context: 67667514 Total unmethylated C's in CHH context: 201787783 Total unmethylated C's in Unknown context: 4326319 C methylated in CpG context: 64.8% C methylated in CHG context: 3.2% C methylated in CHH context: 4.4% C methylated in unknown context (CN or CHN): 19.2% Bismark completed in 0d 5h 33m 34s