| Variant ID: vg0308157341 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 8157341 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATTAGGCTTAAAAGATTCGTCTCGCGATTTCCCCCATAACTATGCAATTAGTTTTTCTTTTTATCTATATTTAATGCTTCATGCATGTGTCTAAAGATT[T/C]
GATGTGATGTTTTTGGGAAAAAAATTTGGGGAACTAAACGGGCCCTAAACACACCCTTCGGCTGTGTTTAGTTCCTGAAAAAAGTTAGAAGTTTGAAAAA
TTTTTCAAACTTCTAACTTTTTTCAGGAACTAAACACAGCCGAAGGGTGTGTTTAGGGCCCGTTTAGTTCCCCAAATTTTTTTCCCAAAAACATCACATC[A/G]
AATCTTTAGACACATGCATGAAGCATTAAATATAGATAAAAAGAAAAACTAATTGCATAGTTATGGGGGAAATCGCGAGACGAATCTTTTAAGCCTAATT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.30% | 23.60% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 94.60% | 5.40% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 39.00% | 60.80% | 0.20% | 0.00% | NA |
| Aus | 269 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.80% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 88.50% | 11.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.70% | 4.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 29.70% | 70.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 36.30% | 63.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 74.30% | 25.30% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 30.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0308157341 | T -> C | LOC_Os03g14950.1 | downstream_gene_variant ; 2610.0bp to feature; MODIFIER | silent_mutation | Average:47.662; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0308157341 | T -> C | LOC_Os03g14950-LOC_Os03g14980 | intergenic_region ; MODIFIER | silent_mutation | Average:47.662; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0308157341 | 1.78E-06 | NA | mr1917 | 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 |
| vg0308157341 | NA | 5.32E-08 | mr1020_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 |
| vg0308157341 | NA | 4.63E-08 | mr1355_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 |
| vg0308157341 | NA | 8.39E-09 | mr1576_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 |