Bismark report for: /gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_16_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:	74531056
Number of alignments with a unique best hit from the different alignments:	3532069
Mapping efficiency:	4.7%
Sequences with no alignments under any condition:	67728813
Sequences did not map uniquely:	3270174
Sequences which were discarded because genomic sequence could not be extracted:	82

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	758833	((converted) top strand)
CT/GA:	816847	((converted) bottom strand)
GA/CT:	940596	(complementary to (converted) top strand)
GA/GA:	1015711	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	21835046

Total methylated C's in CpG context:	4019431
Total methylated C's in CHG context:	128117
Total methylated C's in CHH context:	950616
Total methylated C's in Unknown context:	97

Total unmethylated C's in CpG context:	986573
Total unmethylated C's in CHG context:	3784804
Total unmethylated C's in CHH context:	11965505
Total unmethylated C's in Unknown context:	373

C methylated in CpG context:	80.3%
C methylated in CHG context:	3.3%
C methylated in CHH context:	7.4%
C methylated in Unknown context (CN or CHN):	20.6%


Bismark completed in 0d 0h 38m 38s