Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_5_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:	47401736
Number of alignments with a unique best hit from the different alignments:	2079533
Mapping efficiency:	4.4%
Sequences with no alignments under any condition:	42966736
Sequences did not map uniquely:	2355467
Sequences which were discarded because genomic sequence could not be extracted:	73

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	426898	((converted) top strand)
CT/GA:	463069	((converted) bottom strand)
GA/CT:	580972	(complementary to (converted) top strand)
GA/GA:	608521	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	12804963

Total methylated C's in CpG context:	1404189
Total methylated C's in CHG context:	61962
Total methylated C's in CHH context:	717589
Total methylated C's in Unknown context:	50

Total unmethylated C's in CpG context:	670203
Total unmethylated C's in CHG context:	2249103
Total unmethylated C's in CHH context:	7701917
Total unmethylated C's in Unknown context:	461

C methylated in CpG context:	67.7%
C methylated in CHG context:	2.7%
C methylated in CHH context:	8.5%
C methylated in Unknown context (CN or CHN):	9.8%


Bismark completed in 0d 0h 24m 25s