| Variant ID: vg0409515250 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515250 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
ATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAAC[T/A]
TGTTATCCCGAGTTCCAATCGGCAAAATCAACTTCCATACAAGTTCACCTTCCGAAAAATCCTTAGGCACTACTTTCTTGTTATAATGCCTAGCAACTCG
CGAGTTGCTAGGCATTATAACAAGAAAGTAGTGCCTAAGGATTTTTCGGAAGGTGAACTTGTATGGAAGTTGATTTTGCCGATTGGAACTCGGGATAACA[A/T]
GTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.40% | 0.00% | 0.19% | 8.40% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 74.50% | 0.00% | 0.60% | 24.87% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 34.50% | 0.00% | 1.39% | 64.09% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.83% | 17.43% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515250 | T -> A | LOC_Os04g17380.1 | missense_variant ; p.Lys119Met; MODERATE | N | Average:31.518; most accessible tissue: Minghui63 young leaf, score: 50.756 | N | N | N | N |
| vg0409515250 | T -> A | LOC_Os04g17370.1 | downstream_gene_variant ; 571.0bp to feature; MODIFIER | N | Average:31.518; most accessible tissue: Minghui63 young leaf, score: 50.756 | N | N | N | N |
| vg0409515250 | T -> A | LOC_Os04g17390.1 | downstream_gene_variant ; 1229.0bp to feature; MODIFIER | N | Average:31.518; most accessible tissue: Minghui63 young leaf, score: 50.756 | N | N | N | N |
| vg0409515250 | T -> A | LOC_Os04g17400.1 | downstream_gene_variant ; 3711.0bp to feature; MODIFIER | N | Average:31.518; most accessible tissue: Minghui63 young leaf, score: 50.756 | N | N | N | N |