| Variant ID: vg0335309939 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35309939 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 76. )
TACGCAGTGTAGAGTTTGTAATTAAATGCATAATGCTCCAATTGTCTCTTTCCAACCTCCTTTCGAAACCGAAATGAAGGAAATGATGCCTCAGTGCTCA[G/A]
TGCTTACTTTAGTACTCTCTATTCTATGAATTTAGACACGTAAAGCACATATATACATCAAAACAGCCGAAATTCTGACAAATCGACCTTTAATAAAATT
AATTTTATTAAAGGTCGATTTGTCAGAATTTCGGCTGTTTTGATGTATATATGTGCTTTACGTGTCTAAATTCATAGAATAGAGAGTACTAAAGTAAGCA[C/T]
TGAGCACTGAGGCATCATTTCCTTCATTTCGGTTTCGAAAGGAGGTTGGAAAGAGACAATTGGAGCATTATGCATTTAATTACAAACTCTACACTGCGTA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.80% | 24.10% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 63.40% | 36.50% | 0.14% | 0.00% | NA |
| All Japonica | 1512 | 99.60% | 0.30% | 0.07% | 0.00% | NA |
| Aus | 269 | 60.20% | 39.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 78.30% | 21.50% | 0.17% | 0.00% | NA |
| Indica II | 465 | 41.70% | 57.80% | 0.43% | 0.00% | NA |
| Indica III | 913 | 68.70% | 31.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 58.80% | 41.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 22.20% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0335309939 | G -> A | LOC_Os03g62330.1 | 3_prime_UTR_variant ; 370.0bp to feature; MODIFIER | silent_mutation | Average:66.344; most accessible tissue: Minghui63 root, score: 82.185 | N | N | N | N |
| vg0335309939 | G -> A | LOC_Os03g62314.1 | upstream_gene_variant ; 553.0bp to feature; MODIFIER | silent_mutation | Average:66.344; most accessible tissue: Minghui63 root, score: 82.185 | N | N | N | N |
| vg0335309939 | G -> A | LOC_Os03g62340.1 | downstream_gene_variant ; 2512.0bp to feature; MODIFIER | silent_mutation | Average:66.344; most accessible tissue: Minghui63 root, score: 82.185 | N | N | N | N |