What does *STAR* in ALT stand for

[jielab]

Hi, there:

I used snp-sites to generate a VCF file for ~2 million SARS-COV-2 genome FASTA file that I downloaded from GISAID.

Below is the first record:

I also manually extracted this first record and run a tabulation and got the following:
343927 0
1682817 1
2 2
4 3
5 4
6 5
2 6
4 7

I think 0 is for the REF, while 1-7 are for the 7 ALT alleles (*, A, K, C, S, T, Y) respectively.
But I am not sure that is exactly the first ALT allele * ? It has a count of 1682817.

Thank you very much & best regadrs,
Jie

[pamelacamejom]

Did you get an answer to this question?

[ShriramHPatel]

From what I know, * indicates gap at that position for that genome.
Hope that helps.

[Lewis-W-S-Fisher]

I've notice that sometimes this is just low depth. Do you know what depth is classed as a gap?