| Variant ID: vg0301241360 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 1241360 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCAAGCTCAAGATCTCGAGCAAGGCAAGCCACCTTTGAACATCTTGAGCCTATATCTGAACTTAATTATGTTGCTTGAAAAAAATATTATGCATTGATA[G/A]
GATCGCACTTAATTTGCTTGTCCCGTCTGCAAGGCAGATTGGCGAACCTACCTAATTTGTTGCATCTGATCCTTCCTTTGTTAATTGTTATACCATGTTC
GAACATGGTATAACAATTAACAAAGGAAGGATCAGATGCAACAAATTAGGTAGGTTCGCCAATCTGCCTTGCAGACGGGACAAGCAAATTAAGTGCGATC[C/T]
TATCAATGCATAATATTTTTTTCAAGCAACATAATTAAGTTCAGATATAGGCTCAAGATGTTCAAAGGTGGCTTGCCTTGCTCGAGATCTTGAGCTTGAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.50% | 1.60% | 22.07% | 34.79% | NA |
| All Indica | 2759 | 7.20% | 0.00% | 35.85% | 56.87% | NA |
| All Japonica | 1512 | 93.50% | 5.00% | 1.32% | 0.20% | NA |
| Aus | 269 | 87.00% | 0.00% | 6.69% | 6.32% | NA |
| Indica I | 595 | 9.70% | 0.00% | 18.49% | 71.76% | NA |
| Indica II | 465 | 8.40% | 0.00% | 34.62% | 56.99% | NA |
| Indica III | 913 | 3.10% | 0.00% | 50.49% | 46.44% | NA |
| Indica Intermediate | 786 | 9.50% | 0.10% | 32.70% | 57.63% | NA |
| Temperate Japonica | 767 | 89.20% | 8.10% | 2.48% | 0.26% | NA |
| Tropical Japonica | 504 | 98.20% | 1.40% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 5.21% | 31.25% | NA |
| Intermediate | 90 | 60.00% | 0.00% | 12.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0301241360 | G -> A | LOC_Os03g03034.3 | downstream_gene_variant ; 901.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0301241360 | G -> A | LOC_Os03g03034.5 | downstream_gene_variant ; 2747.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0301241360 | G -> A | LOC_Os03g03034.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0301241360 | G -> A | LOC_Os03g03034.4 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0301241360 | G -> A | LOC_Os03g03034.2 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0301241360 | G -> 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 |
|---|---|---|---|---|---|---|
| vg0301241360 | NA | 1.71E-06 | mr1354 | 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 |
| vg0301241360 | NA | 8.57E-06 | mr1902_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 |
| vg0301241360 | 3.31E-06 | 3.31E-06 | mr1945_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 |