| Variant ID: vg1007739482 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7739482 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )
ATTTTACTGCAGCTAGTCATTTGTTGGCACACACAATTTGAACAAAAAAATTATTACACCTCACAAAACTGTATTTATAATTGCATGCATGTACTAAATT[T/G]
CAGATAATACCAATTGTAGGCAAAATTGTTGGTTCAAAATATTTATGGTCAAGTGTACGTACCGCATTCTTGCTTTCCCACCACTCATCATCGGCAACAA
TTGTTGCCGATGATGAGTGGTGGGAAAGCAAGAATGCGGTACGTACACTTGACCATAAATATTTTGAACCAACAATTTTGCCTACAATTGGTATTATCTG[A/C]
AATTTAGTACATGCATGCAATTATAAATACAGTTTTGTGAGGTGTAATAATTTTTTTGTTCAAATTGTGTGTGCCAACAAATGACTAGCTGCAGTAAAAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.60% | 0.10% | 0.23% | 6.07% | NA |
| All Indica | 2759 | 99.30% | 0.00% | 0.14% | 0.58% | NA |
| All Japonica | 1512 | 81.50% | 0.40% | 0.46% | 17.66% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 0.00% | 0.43% | 1.29% | NA |
| Indica III | 913 | 99.50% | 0.00% | 0.00% | 0.55% | NA |
| Indica Intermediate | 786 | 99.10% | 0.00% | 0.25% | 0.64% | NA |
| Temperate Japonica | 767 | 82.30% | 0.00% | 0.52% | 17.21% | NA |
| Tropical Japonica | 504 | 83.10% | 1.20% | 0.40% | 15.28% | NA |
| Japonica Intermediate | 241 | 75.50% | 0.00% | 0.41% | 24.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007739482 | T -> G | LOC_Os10g14280.1 | upstream_gene_variant ; 1469.0bp to feature; MODIFIER | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007739482 | T -> G | LOC_Os10g14270.1 | downstream_gene_variant ; 3425.0bp to feature; MODIFIER | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007739482 | T -> G | LOC_Os10g14295.1 | downstream_gene_variant ; 1848.0bp to feature; MODIFIER | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007739482 | T -> G | LOC_Os10g14290.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1007739482 | T -> DEL | N | N | silent_mutation | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |