Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//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 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	605809374
Number of alignments with a unique best hit from the different alignments:	185847297
Mapping efficiency:	30.7%
Sequences with no alignments under any condition:	176357696
Sequences did not map uniquely:	243604381
Sequences which were discarded because genomic sequence could not be extracted:	188442

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	42572282	((converted) top strand)
CT/GA:	42250651	((converted) bottom strand)
GA/CT:	50633709	(complementary to (converted) top strand)
GA/GA:	50202213	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1155350419

Total methylated C's in CpG context:	175386903
Total methylated C's in CHG context:	5220316
Total methylated C's in CHH context:	61488338
Total methylated C's in Unknown context:	32115

Total unmethylated C's in CpG context:	30952288
Total unmethylated C's in CHG context:	231484923
Total unmethylated C's in CHH context:	650817651
Total unmethylated C's in Unknown context:	213338

C methylated in CpG context:	85.0%
C methylated in CHG context:	2.2%
C methylated in CHH context:	8.6%
C methylated in Unknown context (CN or CHN):	13.1%


Bismark completed in 0d 12h 39m 50s