| Variant ID: vg0714435991 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14435991 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 127. )
GATACATCAGACCGAGTTCATCACCATGGGGAGCTCCTGTTATCTTTGTAGAAAAGAAAGACCATACCCAGAGGATGTGTGTGGACTATCGCGCACTTAA[C/T]
GATGTGACTATCAAGAATAAGTATCCACTGCCTAGGATTGATGATTTGTTTGATCAACTTAAAGGTGCCACCGTTTTCTCCAAGATAGATCTTCGATCAG
CTGATCGAAGATCTATCTTGGAGAAAACGGTGGCACCTTTAAGTTGATCAAACAAATCATCAATCCTAGGCAGTGGATACTTATTCTTGATAGTCACATC[G/A]
TTAAGTGCGCGATAGTCCACACACATCCTCTGGGTATGGTCTTTCTTTTCTACAAAGATAACAGGAGCTCCCCATGGTGATGAACTCGGTCTGATGTATC
| 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 | 62.80% | 2.10% | 9.27% | 25.79% | NA |
| All Indica | 2759 | 46.20% | 2.80% | 14.35% | 36.61% | NA |
| All Japonica | 1512 | 93.30% | 1.10% | 1.98% | 3.64% | NA |
| Aus | 269 | 48.00% | 0.70% | 2.23% | 49.07% | NA |
| Indica I | 595 | 56.30% | 1.20% | 7.06% | 35.46% | NA |
| Indica II | 465 | 56.30% | 3.20% | 12.26% | 28.17% | NA |
| Indica III | 913 | 26.60% | 3.90% | 21.47% | 47.97% | NA |
| Indica Intermediate | 786 | 55.30% | 2.50% | 12.85% | 29.26% | NA |
| Temperate Japonica | 767 | 97.90% | 0.30% | 0.52% | 1.30% | NA |
| Tropical Japonica | 504 | 95.80% | 0.40% | 0.60% | 3.17% | NA |
| Japonica Intermediate | 241 | 73.00% | 5.40% | 9.54% | 12.03% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 2.08% | 11.46% | NA |
| Intermediate | 90 | 78.90% | 4.40% | 4.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714435991 | C -> DEL | LOC_Os07g25270.1 | N | frameshift_variant | Average:8.683; most accessible tissue: Callus, score: 36.028 | N | N | N | N |
| vg0714435991 | C -> T | LOC_Os07g25270.1 | synonymous_variant ; p.Asn198Asn; LOW | synonymous_codon | Average:8.683; most accessible tissue: Callus, score: 36.028 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714435991 | 5.76E-06 | 1.95E-07 | mr1308_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 |
| vg0714435991 | 8.45E-06 | NA | mr1745_2 | 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 |
| vg0714435991 | 1.25E-07 | 1.25E-07 | mr1853_2 | 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 |
| vg0714435991 | NA | 1.62E-06 | mr1942_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 |