| Variant ID: vg1220960393 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20960393 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )
AGCTAACATGAGTTTAATTCCAAAATTCACTTTGGTAAAAGGTTCCAAGTGCCATACTTGTGTTCAATCGAAACAACCTCGCAAGCCTCACAAGGCATCT[G/A]
AGGCGAGGAATTTGGCACCTCTAGAACTTGTTCATTCCGATTTGTGCGAAATGAACGGCGTGTTGACTAAAGGGGGAAAGAAATATTTCATGACACTGAT
ATCAGTGTCATGAAATATTTCTTTCCCCCTTTAGTCAACACGCCGTTCATTTCGCACAAATCGGAATGAACAAGTTCTAGAGGTGCCAAATTCCTCGCCT[C/T]
AGATGCCTTGTGAGGCTTGCGAGGTTGTTTCGATTGAACACAAGTATGGCACTTGGAACCTTTTACCAAAGTGAATTTTGGAATTAAACTCATGTTAGCT
| 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 | 19.20% | 3.00% | 28.40% | 49.43% | NA |
| All Indica | 2759 | 31.90% | 4.50% | 35.45% | 28.09% | NA |
| All Japonica | 1512 | 1.10% | 0.60% | 15.74% | 82.61% | NA |
| Aus | 269 | 0.00% | 0.40% | 36.06% | 63.57% | NA |
| Indica I | 595 | 27.90% | 2.90% | 26.72% | 42.52% | NA |
| Indica II | 465 | 32.90% | 6.90% | 32.90% | 27.31% | NA |
| Indica III | 913 | 34.40% | 4.80% | 41.62% | 19.17% | NA |
| Indica Intermediate | 786 | 31.60% | 4.10% | 36.39% | 27.99% | NA |
| Temperate Japonica | 767 | 0.90% | 0.30% | 7.56% | 91.26% | NA |
| Tropical Japonica | 504 | 1.40% | 1.40% | 23.21% | 74.01% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.00% | 26.14% | 73.03% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 8.33% | 89.58% | NA |
| Intermediate | 90 | 10.00% | 5.60% | 23.33% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220960393 | G -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1220960393 | G -> A | LOC_Os12g34580.1 | missense_variant ; p.Glu593Lys; MODERATE | nonsynonymous_codon ; E593K | Average:4.64; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.04 |