Bismark report for: hard-trimmed-2112_lane1_ACAGTG_L001_R1.fastq (version: v0.16.3)
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 /home/srlab/Documents/C-virginica-BSSeq/genome/ with the specified options: -q -N 1 --score-min L,0,-0.2 --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	12197930
Number of alignments with a unique best hit from the different alignments:	3456338
Mapping efficiency:	28.3%
Sequences with no alignments under any condition:	5760842
Sequences did not map uniquely:	2980750
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:	181719	((converted) top strand)
CT/GA:	166362	((converted) bottom strand)
GA/CT:	1588675	(complementary to (converted) top strand)
GA/GA:	1519582	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	61813350

Total methylated C's in CpG context:	12572131
Total methylated C's in CHG context:	4005979
Total methylated C's in CHH context:	12350257
Total methylated C's in Unknown context:	0

Total unmethylated C's in CpG context:	2271987
Total unmethylated C's in CHG context:	12442077
Total unmethylated C's in CHH context:	18170919
Total unmethylated C's in Unknown context:	5

C methylated in CpG context:	84.7%
C methylated in CHG context:	24.4%
C methylated in CHH context:	40.5%
C methylated in Unknown context (CN or CHN):	0.0%