Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_1_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:	46792286
Number of alignments with a unique best hit from the different alignments:	14534760
Mapping efficiency:	31.1%
Sequences with no alignments under any condition:	14155170
Sequences did not map uniquely:	18102356
Sequences which were discarded because genomic sequence could not be extracted:	1

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	3291229	((converted) top strand)
CT/GA:	3266810	((converted) bottom strand)
GA/CT:	4005984	(complementary to (converted) top strand)
GA/GA:	3970736	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	88484060

Total methylated C's in CpG context:	11703467
Total methylated C's in CHG context:	417556
Total methylated C's in CHH context:	5009940
Total methylated C's in Unknown context:	3647

Total unmethylated C's in CpG context:	2470410
Total unmethylated C's in CHG context:	17414271
Total unmethylated C's in CHH context:	51468416
Total unmethylated C's in Unknown context:	25966

C methylated in CpG context:	82.6%
C methylated in CHG context:	2.3%
C methylated in CHH context:	8.9%
C methylated in Unknown context (CN or CHN):	12.3%


Bismark completed in 0d 1h 3m 28s