Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_12_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-bs/v082/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	59459431
Number of alignments with a unique best hit from the different alignments:	2728328
Mapping efficiency:	4.6%
Sequences with no alignments under any condition:	53907751
Sequences did not map uniquely:	2823352
Sequences which were discarded because genomic sequence could not be extracted:	84

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	555991	((converted) top strand)
CT/GA:	602078	((converted) bottom strand)
GA/CT:	756652	(complementary to (converted) top strand)
GA/GA:	813523	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	16759013

Total methylated C's in CpG context:	1970106
Total methylated C's in CHG context:	81593
Total methylated C's in CHH context:	852411
Total methylated C's in Unknown context:	54

Total unmethylated C's in CpG context:	816317
Total unmethylated C's in CHG context:	3000835
Total unmethylated C's in CHH context:	10037751
Total unmethylated C's in Unknown context:	490

C methylated in CpG context:	70.7%
C methylated in CHG context:	2.6%
C methylated in CHH context:	7.8%
C methylated in Unknown context (CN or CHN):	9.9%


Bismark completed in 0d 0h 30m 37s