| Variant ID: vg1119557203 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19557203 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AATGCTTTCTATATATAAATGTATTGCAAAACTGTTTTAAAGTCCAATTTTCAACATAATTCATACACTGATAGAGAAACCATCTTTGGTCGGTCGACCC[C/A]
AATCCACAATAGTCCCGGTTCCATTAAAAACCGGGACAAAATGATTTTTAGTCCCGGTTAATAAGAGGAAGATCTTTAGTCCCGGTTGTTGTTACCAACC
GGTTGGTAACAACAACCGGGACTAAAGATCTTCCTCTTATTAACCGGGACTAAAAATCATTTTGTCCCGGTTTTTAATGGAACCGGGACTATTGTGGATT[G/T]
GGGTCGACCGACCAAAGATGGTTTCTCTATCAGTGTATGAATTATGTTGAAAATTGGACTTTAAAACAGTTTTGCAATACATTTATATATAGAAAGCATT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.10% | 32.50% | 0.49% | 0.00% | NA |
| All Indica | 2759 | 96.80% | 2.80% | 0.47% | 0.00% | NA |
| All Japonica | 1512 | 11.40% | 88.20% | 0.46% | 0.00% | NA |
| Aus | 269 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.80% | 2.20% | 1.01% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.50% | 0.22% | 0.00% | NA |
| Indica III | 913 | 98.60% | 1.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 93.80% | 5.60% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 7.60% | 91.90% | 0.52% | 0.00% | NA |
| Tropical Japonica | 504 | 12.30% | 87.30% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 21.60% | 78.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 24.00% | 76.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 55.60% | 41.10% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1119557203 | C -> A | LOC_Os11g33070.1 | upstream_gene_variant ; 2347.0bp to feature; MODIFIER | silent_mutation | Average:30.669; most accessible tissue: Callus, score: 59.439 | N | N | N | N |
| vg1119557203 | C -> A | LOC_Os11g33070-LOC_Os11g33080 | intergenic_region ; MODIFIER | silent_mutation | Average:30.669; most accessible tissue: Callus, score: 59.439 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119557203 | NA | 2.80E-12 | mr1205 | 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 |
| vg1119557203 | NA | 4.41E-08 | mr1514 | 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 |
| vg1119557203 | NA | 1.38E-10 | mr1775 | 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 |
| vg1119557203 | 1.48E-06 | NA | mr1334_2 | 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 |