| Variant ID: vg0609445027 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9445027 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.18, others allele: 0.00, population size: 80. )
GATGGTGATCGAGTGAGAGACGAGGGATTATATAGGTTCGGGCCGCTAGGGAGCGTAATACCCTACTCTTGTGTGTGGAATTATGCTTGTGCTGTTACAA[G/A]
AAAACTCAAACCCTAGGGAACCGGTCGGCTAGTTCTCTCCTAAGGTTCAAGCTTTCCCCAAATCGTCCTTCTACTCAGTGGGCAAGGTCCTCCTTTTATA
TATAAAAGGAGGACCTTGCCCACTGAGTAGAAGGACGATTTGGGGAAAGCTTGAACCTTAGGAGAGAACTAGCCGACCGGTTCCCTAGGGTTTGAGTTTT[C/T]
TTGTAACAGCACAAGCATAATTCCACACACAAGAGTAGGGTATTACGCTCCCTAGCGGCCCGAACCTATATAATCCCTCGTCTCTCACTCGATCACCATC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.60% | 18.60% | 4.38% | 34.43% | NA |
| All Indica | 2759 | 70.30% | 13.80% | 5.29% | 10.58% | NA |
| All Japonica | 1512 | 2.10% | 31.20% | 2.91% | 63.76% | NA |
| Aus | 269 | 1.90% | 2.60% | 2.60% | 92.94% | NA |
| Indica I | 595 | 82.20% | 3.90% | 4.54% | 9.41% | NA |
| Indica II | 465 | 81.50% | 1.90% | 6.24% | 10.32% | NA |
| Indica III | 913 | 52.90% | 30.70% | 5.59% | 10.84% | NA |
| Indica Intermediate | 786 | 74.90% | 8.80% | 4.96% | 11.32% | NA |
| Temperate Japonica | 767 | 1.80% | 55.00% | 3.00% | 40.16% | NA |
| Tropical Japonica | 504 | 2.00% | 5.80% | 2.18% | 90.08% | NA |
| Japonica Intermediate | 241 | 3.30% | 8.70% | 4.15% | 83.82% | NA |
| VI/Aromatic | 96 | 4.20% | 2.10% | 4.17% | 89.58% | NA |
| Intermediate | 90 | 36.70% | 17.80% | 6.67% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609445027 | G -> A | LOC_Os06g16460-LOC_Os06g16470 | intergenic_region ; MODIFIER | silent_mutation | Average:54.576; most accessible tissue: Zhenshan97 young leaf, score: 81.6 | N | N | N | N |
| vg0609445027 | G -> DEL | N | N | silent_mutation | Average:54.576; most accessible tissue: Zhenshan97 young leaf, score: 81.6 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0609445027 | 4.14E-06 | NA | mr1021 | 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 |
| vg0609445027 | 7.70E-06 | NA | mr1477 | 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 |
| vg0609445027 | 4.54E-06 | NA | mr1218_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 |
| vg0609445027 | NA | 3.67E-08 | mr1570_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 |