| Variant ID: vg0720881549 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 20881549 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, G: 0.13, others allele: 0.00, population size: 32. )
ACTATAAATAAGATATCTCTAAACACATGTTTTGTTGTAGTGTATCATTACGGTCCAAAACACATCTGACCGGGTTGATTGCCTTGCGTGGCGGTCCAAC[T/G]
TGGCAACATATTTGCATTTTGGCCCCCCGCATTTTACTTTCCTCGCGTATCCTACCCCCTTCTTCCCCAAATCTTCTTCTCTACCCACGGTGGCTACTGC
GCAGTAGCCACCGTGGGTAGAGAAGAAGATTTGGGGAAGAAGGGGGTAGGATACGCGAGGAAAGTAAAATGCGGGGGGCCAAAATGCAAATATGTTGCCA[A/C]
GTTGGACCGCCACGCAAGGCAATCAACCCGGTCAGATGTGTTTTGGACCGTAATGATACACTACAACAAAACATGTGTTTAGAGATATCTTATTTATAGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.90% | 26.10% | 3.89% | 37.11% | NA |
| All Indica | 2759 | 30.80% | 10.50% | 5.62% | 53.06% | NA |
| All Japonica | 1512 | 39.20% | 46.90% | 1.06% | 12.90% | NA |
| Aus | 269 | 1.50% | 73.20% | 0.37% | 24.91% | NA |
| Indica I | 595 | 17.00% | 12.10% | 6.55% | 64.37% | NA |
| Indica II | 465 | 27.10% | 7.30% | 2.15% | 63.44% | NA |
| Indica III | 913 | 47.90% | 2.80% | 5.04% | 44.25% | NA |
| Indica Intermediate | 786 | 23.70% | 20.10% | 7.63% | 48.60% | NA |
| Temperate Japonica | 767 | 38.10% | 45.40% | 1.17% | 15.38% | NA |
| Tropical Japonica | 504 | 43.80% | 41.90% | 0.40% | 13.89% | NA |
| Japonica Intermediate | 241 | 32.80% | 62.20% | 2.07% | 2.90% | NA |
| VI/Aromatic | 96 | 80.20% | 5.20% | 12.50% | 2.08% | NA |
| Intermediate | 90 | 34.40% | 36.70% | 0.00% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0720881549 | T -> DEL | LOC_Os07g34840.1 | N | frameshift_variant | Average:46.593; most accessible tissue: Callus, score: 70.962 | N | N | N | N |
| vg0720881549 | T -> G | LOC_Os07g34840.1 | synonymous_variant ; p.Thr27Thr; LOW | synonymous_codon | Average:46.593; most accessible tissue: Callus, score: 70.962 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0720881549 | 5.66E-06 | NA | mr1083 | 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 |
| vg0720881549 | NA | 9.65E-07 | mr1121 | 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 |
| vg0720881549 | 3.42E-07 | 6.72E-08 | mr1301 | 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 |
| vg0720881549 | NA | 9.00E-07 | mr1121_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 |
| vg0720881549 | NA | 6.11E-06 | mr1220_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 |
| vg0720881549 | NA | 5.94E-06 | mr1896_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 |