Bismark report for: /Users/hollie/Documents/Oly_Oyster_DNA_Methylation/Data/MBD/Clean_Joined_Data/zr1394_1_cleaned_all.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 /Users/hollie/Documents/Oly_Oyster_DNA_Methylation/Data/Genome/ with the specified options: -q --score-min L,0,-0.2 --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	62868247
Number of alignments with a unique best hit from the different alignments:	1713170
Mapping efficiency:	2.7%
Sequences with no alignments under any condition:	59571125
Sequences did not map uniquely:	1583952
Sequences which were discarded because genomic sequence could not be extracted:	229

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	885380	((converted) top strand)
CT/GA:	827561	((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
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Total number of C's analysed:	16177545

Total methylated C's in CpG context:	2464619
Total methylated C's in CHG context:	87107
Total methylated C's in CHH context:	653157
Total methylated C's in Unknown context:	355

Total unmethylated C's in CpG context:	630259
Total unmethylated C's in CHG context:	3197432
Total unmethylated C's in CHH context:	9144971
Total unmethylated C's in Unknown context:	2679

C methylated in CpG context:	79.6%
C methylated in CHG context:	2.7%
C methylated in CHH context:	6.7%
C methylated in Unknown context (CN or CHN):	11.7%