Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth13_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth13_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: 100607927 Number of paired-end alignments with a unique best hit: 55001232 Mapping efficiency: 54.7% Sequence pairs with no alignments under any condition: 16534149 Sequence pairs did not map uniquely: 29072546 Sequence pairs which were discarded because genomic sequence could not be extracted: 426 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 13494591 ((converted) top strand) GA/CT/CT: 14062913 (complementary to (converted) top strand) GA/CT/GA: 14015354 (complementary to (converted) bottom strand) CT/GA/GA: 13427948 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2719919989 Total methylated C's in CpG context: 36323118 Total methylated C's in CHG context: 3539648 Total methylated C's in CHH context: 10196744 Total methylated C's in Unknown context: 93810 Total unmethylated C's in CpG context: 530796956 Total unmethylated C's in CHG context: 500985850 Total unmethylated C's in CHH context: 1638077673 Total unmethylated C's in Unknown context: 2924927 C methylated in CpG context: 6.4% C methylated in CHG context: 0.7% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 3.1% Bismark completed in 0d 9h 39m 28s