| Variant ID: vg0302039011 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 2039011 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGCTTGGGTCTCGCAACCCTAAGCACTTGTGTTCTACATTCAATCAATCATGCACAGGAGTAGAGTATTACGCTTCTCAGCGGTCCAAACCTGTATAAAC[C/A]
TCTTTTGTCTCATTGTTTTGGAGGGACCTAACCCCCTCAAGATCATACAGCTCCGGTCACCAAGCCCTCGAATCTCACCCGCTGCCCCCGGCCGAACTCA
TGAGTTCGGCCGGGGGCAGCGGGTGAGATTCGAGGGCTTGGTGACCGGAGCTGTATGATCTTGAGGGGGTTAGGTCCCTCCAAAACAATGAGACAAAAGA[G/T]
GTTTATACAGGTTTGGACCGCTGAGAAGCGTAATACTCTACTCCTGTGCATGATTGATTGAATGTAGAACACAAGTGCTTAGGGTTGCGAGACCCAAGCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.00% | 0.90% | 3.09% | 2.01% | NA |
| All Indica | 2759 | 92.00% | 0.00% | 4.53% | 3.41% | NA |
| All Japonica | 1512 | 96.30% | 2.40% | 1.32% | 0.00% | NA |
| Aus | 269 | 98.10% | 1.50% | 0.37% | 0.00% | NA |
| Indica I | 595 | 75.30% | 0.20% | 13.95% | 10.59% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.00% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 91.10% | 0.00% | 5.09% | 3.82% | NA |
| Temperate Japonica | 767 | 94.00% | 3.40% | 2.61% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302039011 | C -> A | LOC_Os03g04420.1 | downstream_gene_variant ; 1975.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0302039011 | C -> A | LOC_Os03g04410-LOC_Os03g04420 | intergenic_region ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0302039011 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0302039011 | 2.50E-06 | NA | mr1980 | 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 |
| vg0302039011 | NA | 6.65E-06 | mr1980 | 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 |
| vg0302039011 | NA | 1.72E-07 | mr1533_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 |