| Variant ID: vg0403119670 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3119670 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.02, others allele: 0.00, population size: 49. )
TTCGTCCGTGTTCCGTTCGCCGGTTTCGGTTGATCATTTGGGTGATCCCGTATCACGTAGAATTGACTCGTTAAGTCGGTATCTCGTGAGGCCCGCTTGA[C/T]
AGATCAATCTAAGCTATCCGATCTTGGTCAACTCTCGGTCGAGATTAATCTCAGCCGCCCAAAATTAATATAAATCATTTCCTCTCTTTCCAATGGCATA
TATGCCATTGGAAAGAGAGGAAATGATTTATATTAATTTTGGGCGGCTGAGATTAATCTCGACCGAGAGTTGACCAAGATCGGATAGCTTAGATTGATCT[G/A]
TCAAGCGGGCCTCACGAGATACCGACTTAACGAGTCAATTCTACGTGATACGGGATCACCCAAATGATCAACCGAAACCGGCGAACGGAACACGGACGAA
| 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 | 36.60% | 28.70% | 2.94% | 31.74% | NA |
| All Indica | 2759 | 25.00% | 45.60% | 3.62% | 25.81% | NA |
| All Japonica | 1512 | 51.20% | 3.90% | 1.59% | 43.32% | NA |
| Aus | 269 | 66.90% | 2.60% | 2.97% | 27.51% | NA |
| Indica I | 595 | 7.20% | 90.60% | 0.50% | 1.68% | NA |
| Indica II | 465 | 23.20% | 50.10% | 4.09% | 22.58% | NA |
| Indica III | 913 | 31.70% | 18.30% | 4.93% | 45.13% | NA |
| Indica Intermediate | 786 | 31.70% | 40.60% | 4.20% | 23.54% | NA |
| Temperate Japonica | 767 | 68.30% | 4.40% | 1.83% | 25.42% | NA |
| Tropical Japonica | 504 | 27.80% | 2.20% | 1.19% | 68.85% | NA |
| Japonica Intermediate | 241 | 45.60% | 5.80% | 1.66% | 46.89% | NA |
| VI/Aromatic | 96 | 53.10% | 5.20% | 2.08% | 39.58% | NA |
| Intermediate | 90 | 38.90% | 32.20% | 5.56% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403119670 | C -> DEL | N | N | silent_mutation | Average:21.064; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0403119670 | C -> T | LOC_Os04g06010.1 | upstream_gene_variant ; 718.0bp to feature; MODIFIER | silent_mutation | Average:21.064; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0403119670 | C -> T | LOC_Os04g06020.1 | downstream_gene_variant ; 2334.0bp to feature; MODIFIER | silent_mutation | Average:21.064; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| vg0403119670 | C -> T | LOC_Os04g06010-LOC_Os04g06020 | intergenic_region ; MODIFIER | silent_mutation | Average:21.064; most accessible tissue: Zhenshan97 flag leaf, score: 39.979 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403119670 | NA | 5.25E-06 | mr1164 | 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 |
| vg0403119670 | NA | 7.41E-07 | mr1229 | 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 |
| vg0403119670 | 2.76E-06 | 1.49E-07 | mr1523 | 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 |
| vg0403119670 | NA | 2.22E-06 | mr1702_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 |