Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth17_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth17_R2_001_val_2.fq.gz (version: v0.21.0) Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Mcap_Genome/ 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: 81609496 Number of paired-end alignments with a unique best hit: 19134278 Mapping efficiency: 23.4% Sequence pairs with no alignments under any condition: 52654481 Sequence pairs did not map uniquely: 9820737 Sequence pairs which were discarded because genomic sequence could not be extracted: 330 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4723410 ((converted) top strand) GA/CT/CT: 4858697 (complementary to (converted) top strand) GA/CT/GA: 4840347 (complementary to (converted) bottom strand) CT/GA/GA: 4711494 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 831577677 Total methylated C's in CpG context: 20054591 Total methylated C's in CHG context: 1920856 Total methylated C's in CHH context: 7440018 Total methylated C's in Unknown context: 575569 Total unmethylated C's in CpG context: 122054673 Total unmethylated C's in CHG context: 145329316 Total unmethylated C's in CHH context: 534778223 Total unmethylated C's in Unknown context: 2700843 C methylated in CpG context: 14.1% C methylated in CHG context: 1.3% C methylated in CHH context: 1.4% C methylated in unknown context (CN or CHN): 17.6% Bismark completed in 0d 4h 14m 43s