Lower case characters in FASTa reference sequence

[foxyg]

Hi, I have noticed in HG19, there are sometimes a segment of sequence that are in lower case? Does this have a special meaning?

Thanks

[swbarnes2]

Often, sequence in loweracse is repetative. It's been soft masked so you can distinguish it from unique sequence

[foxyg]

What about those characters masked with "N", I thought those mean repeats too?

BTW how does aligner like BWA take care "N"s, if it sees Ns in the reference does it automatically ignore those segment?

[nilshomer]

BTW how does aligner like BWA take care "N"s, if it sees Ns in the reference does it automatically ignore those segment?

Hint: it is in the BWA paper.

[foxyg]

Can you kindly point out which paper it is please?

[nilshomer]

Teach a human to fish...