| Variant ID: vg0715976780 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15976780 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 104. )
CCCAATCCAACAGGTCGCGCAACCGATCCAGCAAACACCACCAAGTCGGCCGGTTGTACAGCCGATTCAGCAGACGCCGTTGAGACAGCAGGTCGTTCAG[T/C]
CGACTCGGCAGCAGGGCTTAATGGATGTATCAGCTGGATTCGCATCGCACGCTGGTCAGTGTGCTCCAAATCAGGTTGTCCCAGAGCACTTGATCCATCA
TGATGGATCAAGTGCTCTGGGACAACCTGATTTGGAGCACACTGACCAGCGTGCGATGCGAATCCAGCTGATACATCCATTAAGCCCTGCTGCCGAGTCG[A/G]
CTGAACGACCTGCTGTCTCAACGGCGTCTGCTGAATCGGCTGTACAACCGGCCGACTTGGTGGTGTTTGCTGGATCGGTTGCGCGACCTGTTGGATTGGG
| 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 | 36.00% | 35.30% | 5.88% | 22.81% | NA |
| All Indica | 2759 | 47.90% | 4.20% | 9.68% | 38.17% | NA |
| All Japonica | 1512 | 6.40% | 92.90% | 0.07% | 0.66% | NA |
| Aus | 269 | 93.70% | 6.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 53.60% | 1.80% | 12.94% | 31.60% | NA |
| Indica II | 465 | 17.40% | 5.60% | 6.67% | 70.32% | NA |
| Indica III | 913 | 57.10% | 1.40% | 9.20% | 32.31% | NA |
| Indica Intermediate | 786 | 51.00% | 8.50% | 9.54% | 30.92% | NA |
| Temperate Japonica | 767 | 11.20% | 87.90% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 1.60% | 98.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 1.20% | 97.90% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 9.40% | 90.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 23.30% | 48.90% | 11.11% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715976780 | T -> DEL | LOC_Os07g27420.1 | N | frameshift_variant | Average:22.723; most accessible tissue: Callus, score: 47.93 | N | N | N | N |
| vg0715976780 | T -> C | LOC_Os07g27420.1 | missense_variant ; p.Ser438Pro; MODERATE | nonsynonymous_codon ; S438P | Average:22.723; most accessible tissue: Callus, score: 47.93 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715976780 | 3.93E-06 | 2.10E-07 | mr1344 | 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 |
| vg0715976780 | NA | 1.23E-10 | mr1630 | 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 |
| vg0715976780 | NA | 1.20E-06 | mr1265_2 | 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 |
| vg0715976780 | 5.83E-06 | 5.83E-06 | mr1453_2 | 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 |
| vg0715976780 | 5.25E-06 | 5.25E-06 | mr1528_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 |