| Variant ID: vg0413906303 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 13906303 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 93. )
GCGGAGCCAAATTGCAGAGTTACCTATCGCAGAGATTCCACAGTACAGTTGGGGGTCGGTGGTACTTGCGGCGATATATGCCGGACTATGTGATGCTTGC[A/G,T]
TGAGGAACGGCAAGCAAAGTTCACTCCCTGGATGCCCATTGCTACTTATGTTGTGGGCGCACGAGCACTTCAACATTTGGAGGCCTCAGCTTGACTCGTA
TACGAGTCAAGCTGAGGCCTCCAAATGTTGAAGTGCTCGTGCGCCCACAACATAAGTAGCAATGGGCATCCAGGGAGTGAACTTTGCTTGCCGTTCCTCA[T/C,A]
GCAAGCATCACATAGTCCGGCATATATCGCCGCAAGTACCACCGACCCCCAACTGTACTGTGGAATCTCTGCGATAGGTAACTCTGCAATTTGGCTCCGC
| 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 | 49.00% | 42.70% | 0.34% | 8.00% | NA |
| All Indica | 2759 | 69.20% | 24.30% | 0.33% | 6.16% | NA |
| All Japonica | 1512 | 4.20% | 85.60% | 0.40% | 9.72% | NA |
| Aus | 269 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 44.50% | 46.20% | 0.17% | 9.08% | NA |
| Indica II | 465 | 76.30% | 6.70% | 0.86% | 16.13% | NA |
| Indica III | 913 | 81.70% | 17.50% | 0.22% | 0.55% | NA |
| Indica Intermediate | 786 | 69.20% | 26.00% | 0.25% | 4.58% | NA |
| Temperate Japonica | 767 | 2.90% | 95.20% | 0.26% | 1.69% | NA |
| Tropical Japonica | 504 | 2.80% | 84.90% | 0.40% | 11.90% | NA |
| Japonica Intermediate | 241 | 11.60% | 56.80% | 0.83% | 30.71% | NA |
| VI/Aromatic | 96 | 38.50% | 11.50% | 0.00% | 50.00% | NA |
| Intermediate | 90 | 47.80% | 36.70% | 1.11% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0413906303 | A -> DEL | N | N | silent_mutation | Average:58.803; most accessible tissue: Zhenshan97 young leaf, score: 75.039 | N | N | N | N |
| vg0413906303 | A -> G | LOC_Os04g24274.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.803; most accessible tissue: Zhenshan97 young leaf, score: 75.039 | N | N | N | N |
| vg0413906303 | A -> T | LOC_Os04g24274.1 | intron_variant ; MODIFIER | N | Average:58.803; most accessible tissue: Zhenshan97 young leaf, score: 75.039 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0413906303 | NA | 3.15E-06 | mr1204_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0413906303 | NA | 4.74E-06 | mr1538_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0413906303 | NA | 3.95E-06 | mr1547_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0413906303 | NA | 1.03E-06 | mr1696_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0413906303 | 4.24E-06 | 4.24E-06 | mr1783_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |