| Variant ID: vg0715472268 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15472268 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, T: 0.25, others allele: 0.00, population size: 72. )
TATTTTTGTTAGTCCATGACCATTCGGCAACATAAATATCATGATCACCCTCCTCCTCACTATCACTAACATCAGAGTAATCAACTACATTAACATTAGG[T/C]
TTTTTGTCGAATGGTCTAACAAATTTTTTATCATCTTTAACCCGGCTTTCTTGAGCCAGAGCCCTTTGCATGAGTTGACTAACATCAAGAAATTGTTGGC
GCCAACAATTTCTTGATGTTAGTCAACTCATGCAAAGGGCTCTGGCTCAAGAAAGCCGGGTTAAAGATGATAAAAAATTTGTTAGACCATTCGACAAAAA[A/G]
CCTAATGTTAATGTAGTTGATTACTCTGATGTTAGTGATAGTGAGGAGGAGGGTGATCATGATATTTATGTTGCCGAATGGTCATGGACTAACAAAAATA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.70% | 2.70% | 18.09% | 59.52% | NA |
| All Indica | 2759 | 10.00% | 4.30% | 23.67% | 62.05% | NA |
| All Japonica | 1512 | 40.90% | 0.10% | 0.93% | 58.00% | NA |
| Aus | 269 | 2.60% | 2.20% | 65.06% | 30.11% | NA |
| Indica I | 595 | 17.10% | 0.70% | 3.70% | 78.49% | NA |
| Indica II | 465 | 6.50% | 14.60% | 35.91% | 43.01% | NA |
| Indica III | 913 | 3.50% | 1.10% | 31.33% | 64.07% | NA |
| Indica Intermediate | 786 | 14.10% | 4.70% | 22.65% | 58.52% | NA |
| Temperate Japonica | 767 | 71.40% | 0.10% | 0.39% | 28.03% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 1.19% | 95.44% | NA |
| Japonica Intermediate | 241 | 22.40% | 0.40% | 2.07% | 75.10% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 4.17% | 92.71% | NA |
| Intermediate | 90 | 27.80% | 2.20% | 10.00% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715472268 | T -> DEL | LOC_Os07g26780.1 | N | frameshift_variant | Average:14.59; most accessible tissue: Callus, score: 31.831 | N | N | N | N |
| vg0715472268 | T -> C | LOC_Os07g26780.1 | synonymous_variant ; p.Lys502Lys; LOW | synonymous_codon | Average:14.59; most accessible tissue: Callus, score: 31.831 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715472268 | NA | 7.20E-08 | mr1136 | Ind_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 |
| vg0715472268 | NA | 7.07E-06 | mr1346 | 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 |
| vg0715472268 | 2.51E-06 | 5.60E-07 | mr1780 | Ind_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 |
| vg0715472268 | NA | 3.03E-06 | mr1990 | 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 |