| Variant ID: vg0714395075 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14395075 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 72. )
TGTCAGATAGAGGTAGTCAGTTTACCTCGAAGTTTTGGCAGAAGCTACAAGTAGAGATGGGTACCCGTTTGAATTTCAGTACCGCTTATCACCCTCAAAC[A/T]
GACGGTCAGACAGAAAGAGTAAACCAAATTTTAGAAGACATGTTGAGACCATGTGTTCTAGATTTTGGTAGAAGTTGGGATAAGAATTTGCCGTACGCGG
CCGCGTACGGCAAATTCTTATCCCAACTTCTACCAAAATCTAGAACACATGGTCTCAACATGTCTTCTAAAATTTGGTTTACTCTTTCTGTCTGACCGTC[T/A]
GTTTGAGGGTGATAAGCGGTACTGAAATTCAAACGGGTACCCATCTCTACTTGTAGCTTCTGCCAAAACTTCGAGGTAAACTGACTACCTCTATCTGACA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.70% | 3.10% | 9.27% | 4.93% | NA |
| All Indica | 2759 | 80.20% | 0.50% | 13.01% | 6.27% | NA |
| All Japonica | 1512 | 85.30% | 8.60% | 3.37% | 2.71% | NA |
| Aus | 269 | 87.40% | 0.00% | 6.69% | 5.95% | NA |
| Indica I | 595 | 83.70% | 0.20% | 9.58% | 6.55% | NA |
| Indica II | 465 | 80.20% | 0.20% | 6.88% | 12.69% | NA |
| Indica III | 913 | 76.60% | 0.20% | 19.61% | 3.61% | NA |
| Indica Intermediate | 786 | 81.90% | 1.10% | 11.58% | 5.34% | NA |
| Temperate Japonica | 767 | 84.40% | 13.30% | 1.04% | 1.30% | NA |
| Tropical Japonica | 504 | 95.80% | 0.00% | 1.98% | 2.18% | NA |
| Japonica Intermediate | 241 | 66.40% | 11.60% | 13.69% | 8.30% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 0.00% | 10.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714395075 | A -> DEL | LOC_Os07g25190.1 | N | frameshift_variant | Average:18.919; most accessible tissue: Callus, score: 30.929 | N | N | N | N |
| vg0714395075 | A -> T | LOC_Os07g25190.1 | synonymous_variant ; p.Thr993Thr; LOW | synonymous_codon | Average:18.919; most accessible tissue: Callus, score: 30.929 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714395075 | NA | 8.90E-07 | mr1049_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 |
| vg0714395075 | NA | 4.90E-06 | mr1170_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 |
| vg0714395075 | NA | 1.66E-07 | mr1624_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 |
| vg0714395075 | NA | 7.45E-06 | mr1741_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 |
| vg0714395075 | NA | 3.21E-06 | mr1780_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 |
| vg0714395075 | NA | 5.19E-06 | mr1887_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 |
| vg0714395075 | 3.21E-06 | 3.21E-06 | mr1981_2 | Jap_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 |