Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_4_S12_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_4_S12_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: 25000854 Number of paired-end alignments with a unique best hit: 12778756 Mapping efficiency: 51.1% Sequence pairs with no alignments under any condition: 8760551 Sequence pairs did not map uniquely: 3461547 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: 3219023 ((converted) top strand) GA/CT/CT: 3138879 (complementary to (converted) top strand) GA/CT/GA: 3163050 (complementary to (converted) bottom strand) CT/GA/GA: 3257799 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 580782843 Total methylated C's in CpG context: 33527043 Total methylated C's in CHG context: 1758703 Total methylated C's in CHH context: 13737287 Total methylated C's in Unknown context: 579082 Total unmethylated C's in CpG context: 11058173 Total unmethylated C's in CHG context: 144536545 Total unmethylated C's in CHH context: 376165092 Total unmethylated C's in Unknown context: 1660873 C methylated in CpG context: 75.2% C methylated in CHG context: 1.2% C methylated in CHH context: 3.5% C methylated in unknown context (CN or CHN): 25.9% Bismark completed in 0d 3h 3m 24s