Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_18_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:	55048106
Number of alignments with a unique best hit from the different alignments:	2536705
Mapping efficiency:	4.6%
Sequences with no alignments under any condition:	49739989
Sequences did not map uniquely:	2771412
Sequences which were discarded because genomic sequence could not be extracted:	75

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	501017	((converted) top strand)
CT/GA:	539128	((converted) bottom strand)
GA/CT:	728586	(complementary to (converted) top strand)
GA/GA:	767899	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	15638469

Total methylated C's in CpG context:	2023305
Total methylated C's in CHG context:	79670
Total methylated C's in CHH context:	767014
Total methylated C's in Unknown context:	64

Total unmethylated C's in CpG context:	710544
Total unmethylated C's in CHG context:	2845824
Total unmethylated C's in CHH context:	9212112
Total unmethylated C's in Unknown context:	425

C methylated in CpG context:	74.0%
C methylated in CHG context:	2.7%
C methylated in CHH context:	7.7%
C methylated in Unknown context (CN or CHN):	13.1%


Bismark completed in 0d 0h 28m 25s