Bismark report for: /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_3_S7_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_3_S7_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: 28232841 Number of paired-end alignments with a unique best hit: 14341624 Mapping efficiency: 50.8% Sequence pairs with no alignments under any condition: 9156060 Sequence pairs did not map uniquely: 4735157 Sequence pairs which were discarded because genomic sequence could not be extracted: 4 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 3676893 ((converted) top strand) GA/CT/CT: 3467415 (complementary to (converted) top strand) GA/CT/GA: 3486506 (complementary to (converted) bottom strand) CT/GA/GA: 3710806 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 587216147 Total methylated C's in CpG context: 44899235 Total methylated C's in CHG context: 1781567 Total methylated C's in CHH context: 9682363 Total methylated C's in Unknown context: 747248 Total unmethylated C's in CpG context: 14774290 Total unmethylated C's in CHG context: 148136130 Total unmethylated C's in CHH context: 367942562 Total unmethylated C's in Unknown context: 1901503 C methylated in CpG context: 75.2% C methylated in CHG context: 1.2% C methylated in CHH context: 2.6% C methylated in unknown context (CN or CHN): 28.2% Bismark completed in 0d 2h 56m 13s