Bismark report for: ../data/trimmed-reads/SRR6995995_trimmed.fq.gz (version: v0.25.1)
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 /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/genome/bismark/ with the specified options: -q --score-min L,0,-0.6 --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	31440951
Number of alignments with a unique best hit from the different alignments:	16326352
Mapping efficiency:	51.9%
Sequences with no alignments under any condition:	7192374
Sequences did not map uniquely:	7922225
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	681200	((converted) top strand)
CT/GA:	679514	((converted) bottom strand)
GA/CT:	7435535	(complementary to (converted) top strand)
GA/GA:	7530103	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	323868126

Total methylated C's in CpG context:	48475583
Total methylated C's in CHG context:	17408351
Total methylated C's in CHH context:	57645394
Total methylated C's in Unknown context:	390474

Total unmethylated C's in CpG context:	19594014
Total unmethylated C's in CHG context:	64580248
Total unmethylated C's in CHH context:	116164536
Total unmethylated C's in Unknown context:	905448

C methylated in CpG context:	71.2%
C methylated in CHG context:	21.2%
C methylated in CHH context:	33.2%
C methylated in Unknown context (CN or CHN):	30.1%


Bismark completed in 0d 0h 31m 56s