| Variant ID: vg0406828836 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 6828836 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAGAGGTGGGCCACTGATGGTGATATAATCCTAAGTTAATTTCCTGGGGAGGGTATTCCTCCGTATTTAGCCCTGGTTGTATGGTCATCACGGGCTGTC[G/A]
TAAGGAACTCGGCAGTCAGGGGTGGCTTCTCGAAGTACCAAGAGGGCATCGGATAGAGGGTATTAGCTAGTATATCAGTTAACTAGAATGTATGTATACG
CGTATACATACATTCTAGTTAACTGATATACTAGCTAATACCCTCTATCCGATGCCCTCTTGGTACTTCGAGAAGCCACCCCTGACTGCCGAGTTCCTTA[C/T]
GACAGCCCGTGATGACCATACAACCAGGGCTAAATACGGAGGAATACCCTCCCCAGGAAATTAACTTAGGATTATATCACCATCAGTGGCCCACCTCTCA
| 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 | 57.50% | 10.80% | 3.00% | 28.69% | NA |
| All Indica | 2759 | 34.30% | 16.70% | 4.20% | 44.80% | NA |
| All Japonica | 1512 | 95.90% | 2.60% | 0.93% | 0.60% | NA |
| Aus | 269 | 79.90% | 1.50% | 3.72% | 14.87% | NA |
| Indica I | 595 | 32.30% | 6.20% | 7.06% | 54.45% | NA |
| Indica II | 465 | 51.00% | 14.00% | 3.66% | 31.40% | NA |
| Indica III | 913 | 28.30% | 21.50% | 3.29% | 46.99% | NA |
| Indica Intermediate | 786 | 33.00% | 20.70% | 3.44% | 42.88% | NA |
| Temperate Japonica | 767 | 97.00% | 2.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 96.60% | 1.20% | 1.98% | 0.20% | NA |
| Japonica Intermediate | 241 | 90.90% | 4.60% | 1.24% | 3.32% | NA |
| VI/Aromatic | 96 | 41.70% | 1.00% | 1.04% | 56.25% | NA |
| Intermediate | 90 | 72.20% | 7.80% | 1.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0406828836 | G -> DEL | N | N | silent_mutation | Average:21.326; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
| vg0406828836 | G -> A | LOC_Os04g12380.1 | downstream_gene_variant ; 749.0bp to feature; MODIFIER | silent_mutation | Average:21.326; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
| vg0406828836 | G -> A | LOC_Os04g12370-LOC_Os04g12380 | intergenic_region ; MODIFIER | silent_mutation | Average:21.326; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0406828836 | NA | 2.56E-06 | mr1014 | 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 |
| vg0406828836 | NA | 5.01E-08 | mr1015 | 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 |
| vg0406828836 | NA | 2.34E-06 | mr1166 | 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 |
| vg0406828836 | NA | 1.84E-06 | mr1181 | 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 |
| vg0406828836 | 3.99E-06 | 3.99E-06 | mr1379 | 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 |
| vg0406828836 | NA | 3.02E-06 | mr1930 | 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 |