Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_4_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/v98/ with the specified options: -q --score-min L,0,-0.2 -p 4 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	44905078
Number of alignments with a unique best hit from the different alignments:	13872301
Mapping efficiency:	30.9%
Sequences with no alignments under any condition:	13715942
Sequences did not map uniquely:	17316835
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3093739	((converted) top strand)
CT/GA:	3070130	((converted) bottom strand)
GA/CT:	3864472	(complementary to (converted) top strand)
GA/GA:	3843960	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	85006558

Total methylated C's in CpG context:	11729361
Total methylated C's in CHG context:	405370
Total methylated C's in CHH context:	4793316
Total methylated C's in Unknown context:	3754

Total unmethylated C's in CpG context:	1940399
Total unmethylated C's in CHG context:	16871129
Total unmethylated C's in CHH context:	49266983
Total unmethylated C's in Unknown context:	25310

C methylated in CpG context:	85.8%
C methylated in CHG context:	2.3%
C methylated in CHH context:	8.9%
C methylated in Unknown context (CN or CHN):	12.9%


Bismark completed in 0d 0h 59m 56s