Bismark report for: /gscratch/scrubbed/sr320/0620/zr1394_all_s456_trimmed.fq (version: v0.21.0)
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/olurida-genomes/v081/ with the specified options: -q --score-min L,0,-0.2 -p 14 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	1635584275
Number of alignments with a unique best hit from the different alignments:	507562199
Mapping efficiency:	31.0%
Sequences with no alignments under any condition:	477689355
Sequences did not map uniquely:	650332721
Sequences which were discarded because genomic sequence could not be extracted:	496024

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	115629955	((converted) top strand)
CT/GA:	114795254	((converted) bottom strand)
GA/CT:	138900291	(complementary to (converted) top strand)
GA/GA:	137740675	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3127742922

Total methylated C's in CpG context:	450929646
Total methylated C's in CHG context:	14053551
Total methylated C's in CHH context:	169276746
Total methylated C's in Unknown context:	84062

Total unmethylated C's in CpG context:	83521836
Total unmethylated C's in CHG context:	623336476
Total unmethylated C's in CHH context:	1786624667
Total unmethylated C's in Unknown context:	569646

C methylated in CpG context:	84.4%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.7%
C methylated in Unknown context (CN or CHN):	12.9%


Bismark completed in 4d 19h 52m 3s