| Variant ID: vg0919195909 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 19195909 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAAATCAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAACAAGAAGAAGAAGAAGAAGAAGAAGA[T/A]
GATGATGATGATTTAAGTTAAAAAAAACCGCACCGAGGTGTCCGGTGGGTGGGGATGGAGGAGGCGGTATCTGCGCATCCCCGGCCTCGTGGAGGTCGGA
TCCGACCTCCACGAGGCCGGGGATGCGCAGATACCGCCTCCTCCATCCCCACCCACCGGACACCTCGGTGCGGTTTTTTTTAACTTAAATCATCATCATC[A/T]
TCTTCTTCTTCTTCTTCTTCTTCTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGTTGATTTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.00% | 2.90% | 11.72% | 62.40% | NA |
| All Indica | 2759 | 3.40% | 0.90% | 2.75% | 92.97% | NA |
| All Japonica | 1512 | 62.80% | 6.50% | 30.16% | 0.53% | NA |
| Aus | 269 | 0.70% | 1.50% | 0.37% | 97.40% | NA |
| Indica I | 595 | 3.50% | 0.50% | 1.18% | 94.79% | NA |
| Indica II | 465 | 4.10% | 0.20% | 1.08% | 94.62% | NA |
| Indica III | 913 | 2.30% | 1.60% | 4.93% | 91.13% | NA |
| Indica Intermediate | 786 | 4.10% | 0.80% | 2.42% | 92.75% | NA |
| Temperate Japonica | 767 | 76.90% | 3.50% | 19.43% | 0.13% | NA |
| Tropical Japonica | 504 | 43.30% | 8.90% | 47.82% | 0.00% | NA |
| Japonica Intermediate | 241 | 58.50% | 11.20% | 27.39% | 2.90% | NA |
| VI/Aromatic | 96 | 2.10% | 7.30% | 11.46% | 79.17% | NA |
| Intermediate | 90 | 44.40% | 2.20% | 11.11% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0919195909 | T -> DEL | N | N | silent_mutation | Average:58.439; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0919195909 | T -> A | LOC_Os09g32180.1 | upstream_gene_variant ; 4439.0bp to feature; MODIFIER | silent_mutation | Average:58.439; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0919195909 | T -> A | LOC_Os09g32160.1 | downstream_gene_variant ; 4046.0bp to feature; MODIFIER | silent_mutation | Average:58.439; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| vg0919195909 | T -> A | LOC_Os09g32169.1 | intron_variant ; MODIFIER | silent_mutation | Average:58.439; most accessible tissue: Minghui63 panicle, score: 80.641 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0919195909 | NA | 7.18E-06 | mr1676 | 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 |
| vg0919195909 | 3.61E-06 | 3.61E-06 | mr1342_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 |
| vg0919195909 | 4.18E-06 | 1.24E-11 | mr1676_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 |