Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_13_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:	64352550
Number of alignments with a unique best hit from the different alignments:	3006813
Mapping efficiency:	4.7%
Sequences with no alignments under any condition:	58253464
Sequences did not map uniquely:	3092273
Sequences which were discarded because genomic sequence could not be extracted:	83

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	613488	((converted) top strand)
CT/GA:	669500	((converted) bottom strand)
GA/CT:	827743	(complementary to (converted) top strand)
GA/GA:	895999	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	18725396

Total methylated C's in CpG context:	3032628
Total methylated C's in CHG context:	105154
Total methylated C's in CHH context:	863947
Total methylated C's in Unknown context:	102

Total unmethylated C's in CpG context:	833340
Total unmethylated C's in CHG context:	3335556
Total unmethylated C's in CHH context:	10554771
Total unmethylated C's in Unknown context:	418

C methylated in CpG context:	78.4%
C methylated in CHG context:	3.1%
C methylated in CHH context:	7.6%
C methylated in Unknown context (CN or CHN):	19.6%


Bismark completed in 0d 0h 33m 9s