| Variant ID: vg0909074795 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 9074795 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 309. )
CAGAATTTTCCAATAACAAGAAGTGGAGCAGCAAATTAAAAGATGACGAGGTGACCTATTGCTACATTGATTAATGTATCGCATATCATTCATGAATGTT[T/A]
GGAGTTTCCACCTCTCAGTCTTTATATCATTCATCTCCTCCAGCAGTACTGCTCCTTAGCTCTGTCTACATCTTATATCACAATGGCAGGAGGCCGAATA
TATTCGGCCTCCTGCCATTGTGATATAAGATGTAGACAGAGCTAAGGAGCAGTACTGCTGGAGGAGATGAATGATATAAAGACTGAGAGGTGGAAACTCC[A/T]
AACATTCATGAATGATATGCGATACATTAATCAATGTAGCAATAGGTCACCTCGTCATCTTTTAATTTGCTGCTCCACTTCTTGTTATTGGAAAATTCTG
| 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 | 96.80% | 2.10% | 1.12% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 0.50% | 0.80% | 0.00% | NA |
| All Japonica | 1512 | 92.70% | 5.50% | 1.85% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.80% | 2.00% | 3.19% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.30% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 87.40% | 9.60% | 3.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 2.90% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0909074795 | T -> A | LOC_Os09g15030.1 | downstream_gene_variant ; 4849.0bp to feature; MODIFIER | silent_mutation | Average:70.46; most accessible tissue: Callus, score: 81.476 | N | N | N | N |
| vg0909074795 | T -> A | LOC_Os09g15040.1 | intron_variant ; MODIFIER | silent_mutation | Average:70.46; most accessible tissue: Callus, score: 81.476 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0909074795 | NA | 1.85E-06 | mr1531 | 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 |
| vg0909074795 | 5.08E-07 | 5.08E-07 | mr1587 | 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 |
| vg0909074795 | NA | 4.96E-06 | mr1757_2 | 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 |