| Variant ID: vg1115590193 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15590193 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.31, others allele: 0.00, population size: 90. )
AGCGGCCCGATGACGTCCGTCAGAGGGAGGGCCTGTGCAACATGAAGTCACAACACGATCCTGGCAGAAAAGGGGTAATGGAGTCATCGAGTACACTCAC[G/A]
TTGATCGCAGCTTCGCGTTCAGCCGGACCCTTCTCGCAAAGGGGGACGGGGATGTTGCTCGCTGTCACAGGAGCGCTGATCATCACCTGGCCAATGCGGC
GCCGCATTGGCCAGGTGATGATCAGCGCTCCTGTGACAGCGAGCAACATCCCCGTCCCCCTTTGCGAGAAGGGTCCGGCTGAACGCGAAGCTGCGATCAA[C/T]
GTGAGTGTACTCGATGACTCCATTACCCCTTTTCTGCCAGGATCGTGTTGTGACTTCATGTTGCACAGGCCCTCCCTCTGACGGACGTCATCGGGCCGCT
| 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 | 60.40% | 39.00% | 0.28% | 0.30% | NA |
| All Indica | 2759 | 94.60% | 4.50% | 0.43% | 0.51% | NA |
| All Japonica | 1512 | 2.20% | 97.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 61.00% | 39.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.90% | 6.60% | 0.50% | 0.00% | NA |
| Indica II | 465 | 94.80% | 3.70% | 0.00% | 1.51% | NA |
| Indica III | 913 | 98.90% | 0.30% | 0.44% | 0.33% | NA |
| Indica Intermediate | 786 | 90.70% | 8.10% | 0.64% | 0.51% | NA |
| Temperate Japonica | 767 | 1.30% | 98.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 3.60% | 96.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 48.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1115590193 | G -> A | LOC_Os11g27090.1 | splice_region_variant&synonymous_variant ; p.Asn75Asn; LOW | synonymous_codon | Average:53.618; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| vg1115590193 | G -> DEL | LOC_Os11g27090.1 | N | frameshift_variant | Average:53.618; most accessible tissue: Zhenshan97 young leaf, score: 79.783 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1115590193 | NA | 1.09E-08 | mr1595 | 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 |
| vg1115590193 | 2.27E-06 | NA | mr1758_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 |
| vg1115590193 | 1.13E-06 | NA | mr1758_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 |