High methylation value of C under unknown background

[Ldabao233]

Hi, After running the alignment step, the output results left me a bit confused. The value for 'C methylated in Unknown context (CN or CHN): 48.4%' is surprisingly high. What could be the cause of this? Below is my detailed report. Could you help me understand this? Thank you very much!

`Final Alignment report

Sequence pairs analysed in total: 12294002 Number of paired-end alignments with a unique best hit: 8631424 Mapping efficiency: 70.2% Sequence pairs with no alignments under any condition: 3527298 Sequence pairs did not map uniquely: 135280 Sequence pairs which were discarded because genomic sequence could not be extracted: 1

Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 4317974 ((converted) top strand) GA/CT/CT: 0 (complementary to (converted) top strand) GA/CT/GA: 0 (complementary to (converted) bottom strand) CT/GA/GA: 4313449 ((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: 413471771

Total methylated C's in CpG context: 1695099 Total methylated C's in CHG context: 1879403 Total methylated C's in CHH context: 9152581 Total methylated C's in Unknown context: 417730

Total unmethylated C's in CpG context: 61583053 Total unmethylated C's in CHG context: 64183874 Total unmethylated C's in CHH context: 274977761 Total unmethylated C's in Unknown context: 445332

C methylated in CpG context: 2.7% C methylated in CHG context: 2.8% C methylated in CHH context: 3.2% C methylated in Unknown context (CN or CHN): 48.4%

Bismark completed in 0d 0h 52m 20s`