(Metagenome) Kraken2 : What is "x" replacing the genome sequence?

Question

[mimi]

Hello, I'm using the standard Kraken 2 database.

What is meant by "x" character replacing the eukaryotic genome sequence in library.fna that is reference genome?

What is different from N?

CCCAAACGACTxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxACCCCGCACCAAAAAACATCCNNNNNNNNNNNGGCATGTCCGG
AGACTCCAGTTCTTGGAAAGGATGGGGTCATGTCAGGTGGTTCATCGAGGAGGTACCCGC
CGGAGCTGCGTGAGCGGGCGGTGCGGATGGTCGCAGAGATCCGCGGTCAGCACGATTCGG
AGTGGGCAGCGATCAGTGAGGTCGCCCGTCTACTTGGTGTTGGCTGCGCGGAGACGGTGC
GTAAGTGGGTGCGCCAGGCGCAGGTCGATGCCGGCGCACGGCCCGGGACCACGACCGAAG

Thanks

Answer 1

[lieven.sterck]

Not sure if applicable here but often X (or x) is used to hard-mask the sequence (eg. for transposable elements or such), while N (n) is used to denote a gap or unknown base in the sequence.

[mimi]

Thank you for your response! I've got it.