| Variant ID: vg1207212131 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 7212131 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )
GTTGAAGAAACTTTTTCCGCAACCCAACTCCCTGCCAACAAGCACCTATGAAGCGAAGAAGCTTATATGCCCTTTGTCACTGGGTGTGCGAAAGATACAC[G/A]
CGTGTGTTAACAACTGTATCCTATTCCGTAAAGAGTACGAGGATTTGGACAGATGTACAACATGCAAGAATAGTCGATACAAAACAAGCCGTAGCCAGTC
GACTGGCTACGGCTTGTTTTGTATCGACTATTCTTGCATGTTGTACATCTGTCCAAATCCTCGTACTCTTTACGGAATAGGATACAGTTGTTAACACACG[C/T]
GTGTATCTTTCGCACACCCAGTGACAAAGGGCATATAAGCTTCTTCGCTTCATAGGTGCTTGTTGGCAGGGAGTTGGGTTGCGGAAAAAGTTTCTTCAAC
| 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 | 91.80% | 8.20% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 87.40% | 12.50% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 87.40% | 12.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 58.70% | 41.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.40% | 3.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 85.10% | 14.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 3.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1207212131 | G -> A | LOC_Os12g13010.1 | missense_variant ; p.Ala161Thr; MODERATE | nonsynonymous_codon ; A161T | Average:38.222; most accessible tissue: Minghui63 flag leaf, score: 68.675 | unknown | unknown | DELETERIOUS | 0.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1207212131 | NA | 7.54E-06 | mr1024 | 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 |
| vg1207212131 | 6.50E-07 | 1.14E-11 | mr1024_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 |
| vg1207212131 | NA | 3.53E-11 | mr1565_2 | 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 |
| vg1207212131 | 9.29E-07 | 3.56E-14 | mr1565_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 |