Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_14_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:	87834637
Number of alignments with a unique best hit from the different alignments:	4288182
Mapping efficiency:	4.9%
Sequences with no alignments under any condition:	79466280
Sequences did not map uniquely:	4080175
Sequences which were discarded because genomic sequence could not be extracted:	80

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	892242	((converted) top strand)
CT/GA:	966032	((converted) bottom strand)
GA/CT:	1163049	(complementary to (converted) top strand)
GA/GA:	1266779	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	26352415

Total methylated C's in CpG context:	4467852
Total methylated C's in CHG context:	149314
Total methylated C's in CHH context:	1095506
Total methylated C's in Unknown context:	120

Total unmethylated C's in CpG context:	1161113
Total unmethylated C's in CHG context:	4546966
Total unmethylated C's in CHH context:	14931664
Total unmethylated C's in Unknown context:	508

C methylated in CpG context:	79.4%
C methylated in CHG context:	3.2%
C methylated in CHH context:	6.8%
C methylated in Unknown context (CN or CHN):	19.1%


Bismark completed in 0d 0h 45m 17s