Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_3_S15_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_3_S15_R2_001_val_2.fq.gz (version: v0.19.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ 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: 29194972 Number of paired-end alignments with a unique best hit: 14795493 Mapping efficiency: 50.7% Sequence pairs with no alignments under any condition: 10215196 Sequence pairs did not map uniquely: 4184283 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: 3559660 ((converted) top strand) GA/CT/CT: 3827142 (complementary to (converted) top strand) GA/CT/GA: 3833510 (complementary to (converted) bottom strand) CT/GA/GA: 3575176 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 621883200 Total methylated C's in CpG context: 41738884 Total methylated C's in CHG context: 1945186 Total methylated C's in CHH context: 19896009 Total methylated C's in Unknown context: 696548 Total unmethylated C's in CpG context: 12745175 Total unmethylated C's in CHG context: 159795105 Total unmethylated C's in CHH context: 385762841 Total unmethylated C's in Unknown context: 1853736 C methylated in CpG context: 76.6% C methylated in CHG context: 1.2% C methylated in CHH context: 4.9% C methylated in unknown context (CN or CHN): 27.3% Bismark completed in 0d 3h 19m 21s