N_ALLELES is the number of alternate ALT alleles in the VCF file.

The ALT column of a VCF file can contain more than one allele .

E.g: REF is 'T' but the variation was genotyped as 'A' or 'C'.

On this thread from vcftools mailing list: N_ALLELES represents number of different alt alleles + reference allele, and N_CHR is number of chromosomes that have data for that locus (usually #samples_covering_locus x 2).

Hi,

The questions about the meaning of N_CHR still not be answered. And more I encountered the N_CHR value 0 with allele frequency "nan", just like the following example.

CHROM   POS     N_ALLELES       N_CHR   {ALLELE:FREQ}
C162769346      2       3       0       A:-nan  C:-nan  G:-nan

Thank you!