Bismark report for: hard-trimmed-2112_lane1_TGACCA_L001_R1_001.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:	2800289
Number of alignments with a unique best hit from the different alignments:	623273
Mapping efficiency:	22.3%
Sequences with no alignments under any condition:	1588744
Sequences did not map uniquely:	588272
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:	59279	((converted) top strand)
CT/GA:	55305	((converted) bottom strand)
GA/CT:	258437	(complementary to (converted) top strand)
GA/GA:	250252	(complementary to (converted) bottom strand)

Final Cytosine Methylation Report
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Total number of C's analysed:	10412368

Total methylated C's in CpG context:	2215432
Total methylated C's in CHG context:	1428445
Total methylated C's in CHH context:	3781284
Total methylated C's in Unknown context:	3

Total unmethylated C's in CpG context:	261842
Total unmethylated C's in CHG context:	1215969
Total unmethylated C's in CHH context:	1509396
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	89.4%
C methylated in CHG context:	54.0%
C methylated in CHH context:	71.5%
C methylated in Unknown context (CN or CHN):	100.0%