Table 3.
List of the five candidate overlapping ORFs in the 3’ genome region of SARS-CoV-2 (italic characters indicate ORFs predicted by other methods; bold characters indicate ORFs predicted only by the CodScr + SeqComp method).
| Candidate overlapping ORF (length) | Ancestral overlapping gene | Boundaries of candidate overlapping ORF | Shift vs. ancestral gene | P value from CodScr | PLS-DA score | LDA score | LDA-ancestral score | LDA-novel score | Prediction criteria met |
|---|---|---|---|---|---|---|---|---|---|
| ORF3c (126 nt) | ORF3a | 25457–25582 | +1 | 0.04 | −1.46 | −41.89 | 21.48 | 12.76 | 5 |
| ORF3d (174 nt) | ORF3a | 25524–25697 | +2 | 0.02 | −1.32 | −40.44 | −27.80 | −59.59 | 5 |
| ORF9b (294 nt) | N | 28284–28577 | +1 | 0.0001 | −0.52 | −39.17 | 27.12 | 11.56 | 5 |
| ORF-Sh (120 nt) | S | 24051–24170 | +1 | 0.0001 | −0.45 | −37.03 | 37.07 | −1.54 | 5 |
| ORF-Mh (180 nt) | M | 26693–26872 | +2 | 0.003 | −0.02 | −36.26 | −17.74 | −60.62 | 5 |
aBoundaries of the overlapping ORF are referred to the reference genome sequence of SARS-CoV-2 (NC_045512.2).