Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_7_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:	49730113
Number of alignments with a unique best hit from the different alignments:	2247688
Mapping efficiency:	4.5%
Sequences with no alignments under any condition:	45094621
Sequences did not map uniquely:	2387804
Sequences which were discarded because genomic sequence could not be extracted:	64

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	467398	((converted) top strand)
CT/GA:	507622	((converted) bottom strand)
GA/CT:	615887	(complementary to (converted) top strand)
GA/GA:	656717	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	13889878

Total methylated C's in CpG context:	2000903
Total methylated C's in CHG context:	75085
Total methylated C's in CHH context:	662881
Total methylated C's in Unknown context:	58

Total unmethylated C's in CpG context:	635805
Total unmethylated C's in CHG context:	2459263
Total unmethylated C's in CHH context:	8055941
Total unmethylated C's in Unknown context:	331

C methylated in CpG context:	75.9%
C methylated in CHG context:	3.0%
C methylated in CHH context:	7.6%
C methylated in Unknown context (CN or CHN):	14.9%


Bismark completed in 0d 0h 25m 36s