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Old 06-26-2016, 12:16 PM   #1
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Location: USA

Join Date: Jul 2014
Posts: 9
Default snpEFF annotation - "NA"


I am trying to annotate the SNPs for maize samples using snpEff.
In the annotation column or the EFF column in the result vcf file some positions are annotated as “NA”.
But these positions are actually present in the gff file with some gene feature. See example below:

For gene GRMZM2G027219:

2 74716293 NA

The same position falls between an exon in the gff file from which the database is built.

Exon 74716207 74716341
five_prime_UTR 74716207 74716797

My question is why this positon is annotated as NA and not exon or 5’ as shown in the gff file.
There are several other positons that are annotated as NA thought these positions are present in the gff file.

Please if you could explain me in what condition a position will be annotated as “NA”.

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