| Variant ID: vg0709146977 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 9146977 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.02, others allele: 0.00, population size: 119. )
TAGGTGGCGGCGGCCATCAGAGGTTCATCCTTAGCAGAATTGGCTATGGTGAGAGCAAACGCTTGGCCGATCCCAATCTCATCCCAGTGGACTTTCTTAC[T/A]
AGCCGATATGCGTTGGTACCAGGTGGTCCAACTCTTATCAGGGGTAGGCTTTTCGAGAGATGGCCAAGACTTGAAGGTATTCTTCCAGTGACCCAGGTTA
TAACCTGGGTCACTGGAAGAATACCTTCAAGTCTTGGCCATCTCTCGAAAAGCCTACCCCTGATAAGAGTTGGACCACCTGGTACCAACGCATATCGGCT[A/T]
GTAAGAAAGTCCACTGGGATGAGATTGGGATCGGCCAAGCGTTTGCTCTCACCATAGCCAATTCTGCTAAGGATGAACCTCTGATGGCCGCCGCCACCTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.20% | 39.20% | 2.24% | 2.31% | NA |
| All Indica | 2759 | 30.80% | 64.70% | 3.08% | 1.38% | NA |
| All Japonica | 1512 | 93.70% | 1.20% | 0.66% | 4.50% | NA |
| Aus | 269 | 90.30% | 6.70% | 2.97% | 0.00% | NA |
| Indica I | 595 | 67.70% | 25.90% | 3.03% | 3.36% | NA |
| Indica II | 465 | 16.10% | 77.80% | 5.16% | 0.86% | NA |
| Indica III | 913 | 9.60% | 88.50% | 1.64% | 0.22% | NA |
| Indica Intermediate | 786 | 36.30% | 58.70% | 3.56% | 1.53% | NA |
| Temperate Japonica | 767 | 96.60% | 1.40% | 1.04% | 0.91% | NA |
| Tropical Japonica | 504 | 88.50% | 0.80% | 0.00% | 10.71% | NA |
| Japonica Intermediate | 241 | 95.00% | 1.20% | 0.83% | 2.90% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 60.00% | 35.60% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0709146977 | T -> DEL | LOC_Os07g15760.1 | N | frameshift_variant | Average:20.985; most accessible tissue: Minghui63 flower, score: 40.98 | N | N | N | N |
| vg0709146977 | T -> A | LOC_Os07g15760.1 | missense_variant&splice_region_variant ; p.Asn96Tyr; MODERATE | nonsynonymous_codon | Average:20.985; most accessible tissue: Minghui63 flower, score: 40.98 | unknown | unknown | DELETERIOUS | 0.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0709146977 | NA | 7.49E-15 | mr1170 | 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 |
| vg0709146977 | NA | 7.74E-07 | mr1170 | 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 |
| vg0709146977 | NA | 1.66E-14 | mr1316 | 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 |
| vg0709146977 | NA | 4.69E-06 | mr1316 | 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 |
| vg0709146977 | NA | 2.49E-07 | mr1716 | 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 |