# Annotation of SARS-CoV-2 variation

https://github.com/spond/SARS-CoV-2-variation/blob/master/variation/variant-annotation.csv

### Headers

Coord,Ref,Codon,GlobalF,First,Last,Clade0.75,PS,NS,LastSel,Pred,Haplo

1. `Coord` : 0-based genomic coordiante for codon styart
2. `Ref` : Reference codon at this position
3. `Codon` : Alternate codon at this position
4. `GlobalF` : Frequency of this codon in global (GISAID) data
5. `First` : date first sampled
6. `Last` : data last sampled
7. `Clade0.75`: ';' separated list of Pangolin clades where this variant is at 75% or higher. Limited to clades with at least `1000` sequences
8. `PS` : number of sliding windows in which this site was positively selected
9. `NS` : number of sliding windows in which this site was negatively selected
10. `LastSel` : status of selection analysis in the most recent sliding window. `+` - positively selected, `-` - negatively selected, `N` - neutral.
11. `Pred` : evolutionary credibility of this variant
12. `Haplo` : relative rank (scaled to [0,1]) of how many unique haplotypes this variant occurs in. Lower values -- more haplotypes

### Example

1. `Coord` : 442
2. `Ref`: GTT
3. `Codon`: GTC
4. `GlobalF`: 0.050085833016674394
6. `First`: 20200316
7. `Last`: 20210904
8. `Clade0.75`: B.1.177;B.1.177.21;B.1.177.12;B.1.177.7;B.1.177.86;B.1.177.4;B.1.177.81;B.1.177.57;B.1.177.60;B.1.177.45;B.1.177.82;B.1.177.44;B.1.177.35;B.1.177.54;B.1.177.79;B.1.177.16;B.1.177.56;B.1.177.65;B.1.177.15;B.1.177.77;B.1.177.87;B.1.177.8;B.1.177.73;B.1.177.17;B.1.177.10;B.1.177.46
9. `PS` : 12
10. `NS` : 1
11. `LastSel`: +
12. `Pred` : 0.04775157415744558
13. `Haplo` :0.004277421326000611