Bismark report for: ../data/trimmed-reads/SRR6995994_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:	2835345
Number of alignments with a unique best hit from the different alignments:	1191953
Mapping efficiency:	42.0%
Sequences with no alignments under any condition:	908438
Sequences did not map uniquely:	734954
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:	119895	((converted) top strand)
CT/GA:	134912	((converted) bottom strand)
GA/CT:	442850	(complementary to (converted) top strand)
GA/GA:	494296	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	23862948

Total methylated C's in CpG context:	5226320
Total methylated C's in CHG context:	3007685
Total methylated C's in CHH context:	8531556
Total methylated C's in Unknown context:	36442

Total unmethylated C's in CpG context:	778082
Total unmethylated C's in CHG context:	2880476
Total unmethylated C's in CHH context:	3438829
Total unmethylated C's in Unknown context:	28704

C methylated in CpG context:	87.0%
C methylated in CHG context:	51.1%
C methylated in CHH context:	71.3%
C methylated in Unknown context (CN or CHN):	55.9%


Bismark completed in 0d 0h 2m 35s