Bismark report for: ../data/trimmed-reads/SRR6995993_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:	21578440
Number of alignments with a unique best hit from the different alignments:	11084149
Mapping efficiency:	51.4%
Sequences with no alignments under any condition:	5301433
Sequences did not map uniquely:	5192858
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:	470774	((converted) top strand)
CT/GA:	478307	((converted) bottom strand)
GA/CT:	5024925	(complementary to (converted) top strand)
GA/GA:	5110143	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	218245240

Total methylated C's in CpG context:	32500442
Total methylated C's in CHG context:	8246352
Total methylated C's in CHH context:	26330315
Total methylated C's in Unknown context:	221200

Total unmethylated C's in CpG context:	14466369
Total unmethylated C's in CHG context:	47850314
Total unmethylated C's in CHH context:	88851448
Total unmethylated C's in Unknown context:	636641

C methylated in CpG context:	69.2%
C methylated in CHG context:	14.7%
C methylated in CHH context:	22.9%
C methylated in Unknown context (CN or CHN):	25.8%


Bismark completed in 0d 0h 22m 15s