| Variant ID: vg0334098385 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34098385 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 336. )
GTGTTGACGACATCGACGATCGTCCCACTATGGGATCTTTGTGGACACACTGTGAGGTAAATTTTGTTTAATTCGTTTGTGTTCTCATTATGAACAGTTC[C/T,A]
GTATTAGTTCAATACTTTCCTGATATAACTAATCATAACTATTATCTTCTTGCAGCCGAAGTGGGTTAGCGGGACGACGCGTCGTGTGTACACACAGTTC
GAACTGTGTGTACACACGACGCGTCGTCCCGCTAACCCACTTCGGCTGCAAGAAGATAATAGTTATGATTAGTTATATCAGGAAAGTATTGAACTAATAC[G/A,T]
GAACTGTTCATAATGAGAACACAAACGAATTAAACAAAATTTACCTCACAGTGTGTCCACAAAGATCCCATAGTGGGACGATCGTCGATGTCGTCAACAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.50% | 13.40% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 77.50% | 22.40% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 80.00% | 19.30% | 0.67% | 0.00% | NA |
| Indica II | 465 | 84.70% | 15.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 75.20% | 24.60% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 73.80% | 26.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098385 | C -> T | LOC_Os03g59894.1 | downstream_gene_variant ; 1718.0bp to feature; MODIFIER | silent_mutation | Average:47.182; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0334098385 | C -> T | LOC_Os03g59920.1 | downstream_gene_variant ; 1176.0bp to feature; MODIFIER | silent_mutation | Average:47.182; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0334098385 | C -> T | LOC_Os03g59910.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.182; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0334098385 | C -> A | LOC_Os03g59894.1 | downstream_gene_variant ; 1718.0bp to feature; MODIFIER | N | Average:47.182; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0334098385 | C -> A | LOC_Os03g59920.1 | downstream_gene_variant ; 1176.0bp to feature; MODIFIER | N | Average:47.182; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |
| vg0334098385 | C -> A | LOC_Os03g59910.1 | intron_variant ; MODIFIER | N | Average:47.182; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |