Bismark report for: 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:	12260444
Number of alignments with a unique best hit from the different alignments:	3439005
Mapping efficiency:	28.0%
Sequences with no alignments under any condition:	6508309
Sequences did not map uniquely:	2313130
Sequences which were discarded because genomic sequence could not be extracted:	4

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	194297	((converted) top strand)
CT/GA:	177441	((converted) bottom strand)
GA/CT:	1574633	(complementary to (converted) top strand)
GA/GA:	1492630	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	72855963

Total methylated C's in CpG context:	15487306
Total methylated C's in CHG context:	5008319
Total methylated C's in CHH context:	15081081
Total methylated C's in Unknown context:	5

Total unmethylated C's in CpG context:	2557484
Total unmethylated C's in CHG context:	14183192
Total unmethylated C's in CHH context:	20538581
Total unmethylated C's in Unknown context:	78

C methylated in CpG context:	85.8%
C methylated in CHG context:	26.1%
C methylated in CHH context:	42.3%
C methylated in Unknown context (CN or CHN):	6.0%