Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_9_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:	77350922
Number of alignments with a unique best hit from the different alignments:	3614877
Mapping efficiency:	4.7%
Sequences with no alignments under any condition:	69851458
Sequences did not map uniquely:	3884587
Sequences which were discarded because genomic sequence could not be extracted:	89

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	743807	((converted) top strand)
CT/GA:	809937	((converted) bottom strand)
GA/CT:	999563	(complementary to (converted) top strand)
GA/GA:	1061481	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	22085171

Total methylated C's in CpG context:	2591728
Total methylated C's in CHG context:	102822
Total methylated C's in CHH context:	1045017
Total methylated C's in Unknown context:	74

Total unmethylated C's in CpG context:	1010302
Total unmethylated C's in CHG context:	3818600
Total unmethylated C's in CHH context:	13516702
Total unmethylated C's in Unknown context:	741

C methylated in CpG context:	72.0%
C methylated in CHG context:	2.6%
C methylated in CHH context:	7.2%
C methylated in Unknown context (CN or CHN):	9.1%


Bismark completed in 0d 0h 40m 7s