Bismark report for: /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_s1_R1.fastq.gz and /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_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: 32636231 Number of paired-end alignments with a unique best hit: 10389383 Mapping efficiency: 31.8% Sequence pairs with no alignments under any condition: 19378195 Sequence pairs did not map uniquely: 2868653 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 2817892 ((converted) top strand) GA/CT/CT: 2366113 (complementary to (converted) top strand) GA/CT/GA: 2380610 (complementary to (converted) bottom strand) CT/GA/GA: 2824766 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 393776621 Total methylated C's in CpG context: 40612390 Total methylated C's in CHG context: 2982484 Total methylated C's in CHH context: 10534650 Total methylated C's in Unknown context: 1349020 Total unmethylated C's in CpG context: 13936979 Total unmethylated C's in CHG context: 84223643 Total unmethylated C's in CHH context: 241486475 Total unmethylated C's in Unknown context: 5462880 C methylated in CpG context: 74.5% C methylated in CHG context: 3.4% C methylated in CHH context: 4.2% C methylated in unknown context (CN or CHN): 19.8% Bismark completed in 0d 6h 25m 50s