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

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

metagenome sequencing
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updated by Ram Ram • written by mimi • mimi

1 answer

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.

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written by lieven.sterck lieven.sterck

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

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written by mimi • mimi

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