| Variant ID: vg1119007993 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19007993 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.34, others allele: 0.00, population size: 182. )
CGATTTGGGCGGAGTCGCGACACAAATCGATCCGGCTTCTTGAACGCGTACGCTCTTGAGCCCCGCAATCGCAGCACCACATCTCCTCTGGTTATCACCC[G/A]
TGCCGAAATGCGGATGACCTCGCCGAGAAGGCTAATCCCTGTTTGCCAATCGAAGAACACAAACAAGAACGAGATAGAAACAACCAAAATTGCAGATGAA
TTCATCTGCAATTTTGGTTGTTTCTATCTCGTTCTTGTTTGTGTTCTTCGATTGGCAAACAGGGATTAGCCTTCTCGGCGAGGTCATCCGCATTTCGGCA[C/T]
GGGTGATAACCAGAGGAGATGTGGTGCTGCGATTGCGGGGCTCAAGAGCGTACGCGTTCAAGAAGCCGGATCGATTTGTGTCGCGACTCCGCCCAAATCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.20% | 16.20% | 6.54% | 16.06% | NA |
| All Indica | 2759 | 90.00% | 5.90% | 4.02% | 0.04% | NA |
| All Japonica | 1512 | 8.80% | 31.20% | 10.91% | 49.14% | NA |
| Aus | 269 | 77.70% | 21.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 96.60% | 1.70% | 1.68% | 0.00% | NA |
| Indica II | 465 | 90.30% | 3.40% | 6.24% | 0.00% | NA |
| Indica III | 913 | 87.50% | 7.40% | 5.04% | 0.00% | NA |
| Indica Intermediate | 786 | 87.70% | 8.90% | 3.31% | 0.13% | NA |
| Temperate Japonica | 767 | 5.20% | 49.70% | 3.00% | 42.11% | NA |
| Tropical Japonica | 504 | 15.70% | 6.00% | 25.99% | 52.38% | NA |
| Japonica Intermediate | 241 | 5.80% | 24.90% | 4.56% | 64.73% | NA |
| VI/Aromatic | 96 | 9.40% | 57.30% | 23.96% | 9.38% | NA |
| Intermediate | 90 | 65.60% | 17.80% | 10.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1119007993 | G -> A | LOC_Os11g32180.1 | intron_variant ; MODIFIER | silent_mutation | Average:17.426; most accessible tissue: Zhenshan97 root, score: 34.536 | N | N | N | N |
| vg1119007993 | G -> DEL | N | N | silent_mutation | Average:17.426; most accessible tissue: Zhenshan97 root, score: 34.536 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119007993 | 2.83E-06 | 2.83E-06 | mr1320 | Jap_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 |
| vg1119007993 | NA | 5.96E-06 | mr1686 | Jap_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 |
| vg1119007993 | NA | 3.43E-06 | mr1138_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 |
| vg1119007993 | NA | 1.38E-06 | mr1354_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 |
| vg1119007993 | NA | 3.89E-06 | mr1528_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 |