| Variant ID: vg1220960402 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960402 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 313. )
GAGTTTAATTCCAAAATTCACTTTGGTAAAAGGTTCCAAGTGCCATACTTGTGTTCAATCGAAACAACCTCGCAAGCCTCACAAGGCATCTGAGGCGAGG[A/G]
ATTTGGCACCTCTAGAACTTGTTCATTCCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGATAGATGATTG
CAATCATCTATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGGAATGAACAAGTTCTAGAGGTGCCAAAT[T/C]
CCTCGCCTCAGATGCCTTGTGAGGCTTGCGAGGTTGTTTCGATTGAACACAAGTATGGCACTTGGAACCTTTTACCAAAGTGAATTTTGGAATTAAACTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 4.50% | 0.60% | 24.78% | 70.06% | NA |
| All Indica | 2759 | 7.50% | 0.90% | 36.46% | 55.13% | NA |
| All Japonica | 1512 | 0.10% | 0.30% | 8.73% | 90.87% | NA |
| Aus | 269 | 0.40% | 0.40% | 4.46% | 94.80% | NA |
| Indica I | 595 | 4.90% | 0.30% | 28.24% | 66.55% | NA |
| Indica II | 465 | 11.20% | 1.10% | 30.75% | 56.99% | NA |
| Indica III | 913 | 8.10% | 1.10% | 46.00% | 44.80% | NA |
| Indica Intermediate | 786 | 6.70% | 0.90% | 34.99% | 57.38% | NA |
| Temperate Japonica | 767 | 0.10% | 0.00% | 6.26% | 93.61% | NA |
| Tropical Japonica | 504 | 0.20% | 0.80% | 9.33% | 89.68% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 15.35% | 84.65% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 3.30% | 1.10% | 20.00% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960402 | A -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960402 | A -> G | LOC_Os12g34580.1 | missense_variant ; p.Asn596Asp; MODERATE | nonsynonymous_codon | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.02 |