Bismark report for: ../data/trimmed-reads/SRR6995996_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,-0.2 -p 8 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	500000
Number of alignments with a unique best hit from the different alignments:	159658
Mapping efficiency:	31.9%
Sequences with no alignments under any condition:	259915
Sequences did not map uniquely:	80427
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:	8588	((converted) top strand)
CT/GA:	8817	((converted) bottom strand)
GA/CT:	70811	(complementary to (converted) top strand)
GA/GA:	71442	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3222221

Total methylated C's in CpG context:	423326
Total methylated C's in CHG context:	202109
Total methylated C's in CHH context:	684618
Total methylated C's in Unknown context:	1080

Total unmethylated C's in CpG context:	147725
Total unmethylated C's in CHG context:	569371
Total unmethylated C's in CHH context:	1195072
Total unmethylated C's in Unknown context:	1833

C methylated in CpG context:	74.1%
C methylated in CHG context:	26.2%
C methylated in CHH context:	36.4%
C methylated in Unknown context (CN or CHN):	37.1%


Bismark completed in 0d 0h 0m 49s