Bismark report for: hard-trimmed-2112_lane1_CAGATC_R1.fastq (version: v0.16.3)
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
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:	31118991
Number of alignments with a unique best hit from the different alignments:	1820550
Mapping efficiency:	5.9%
Sequences with no alignments under any condition:	27437996
Sequences did not map uniquely:	1860445
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:	931439	((converted) top strand)
CT/GA:	889111	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	30398051

Total methylated C's in CpG context:	4249037
Total methylated C's in CHG context:	5006522
Total methylated C's in CHH context:	16503824
Total methylated C's in Unknown context:	3

Total unmethylated C's in CpG context:	458073
Total unmethylated C's in CHG context:	1436814
Total unmethylated C's in CHH context:	2743781
Total unmethylated C's in Unknown context:	0

C methylated in CpG context:	90.3%
C methylated in CHG context:	77.7%
C methylated in CHH context:	85.7%
C methylated in Unknown context (CN or CHN):	100.0%