| Variant ID: vg1004377181 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4377181 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 111. )
TCTTGGCGCAACTTGAATGCAATGCCGAGCTAGATATGGAACACAAGAAGCTAGCCGATCTCCCAAAATCAATTGAAGAACAAAAATCAAGGCTCAAATC[A/G]
GCTATCAAGAATGTTGCCGACCTAACCAAGTCCCTGAAAGTCATCTCTGGAACTGATGCTCAACATGCCCAAGCTATTGAAGAAAAAGAACAAATTAGGC
GCCTAATTTGTTCTTTTTCTTCAATAGCTTGGGCATGTTGAGCATCAGTTCCAGAGATGACTTTCAGGGACTTGGTTAGGTCGGCAACATTCTTGATAGC[T/C]
GATTTGAGCCTTGATTTTTGTTCTTCAATTGATTTTGGGAGATCGGCTAGCTTCTTGTGTTCCATATCTAGCTCGGCATTGCATTCAAGTTGCGCCAAGA
| 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 | 41.30% | 16.00% | 2.29% | 40.41% | NA |
| All Indica | 2759 | 31.20% | 16.30% | 3.84% | 48.64% | NA |
| All Japonica | 1512 | 67.70% | 1.10% | 0.07% | 31.15% | NA |
| Aus | 269 | 1.50% | 93.30% | 0.00% | 5.20% | NA |
| Indica I | 595 | 35.80% | 42.40% | 1.85% | 20.00% | NA |
| Indica II | 465 | 38.10% | 10.50% | 1.51% | 49.89% | NA |
| Indica III | 913 | 22.10% | 3.30% | 6.24% | 68.35% | NA |
| Indica Intermediate | 786 | 34.10% | 15.30% | 3.94% | 46.69% | NA |
| Temperate Japonica | 767 | 89.40% | 0.30% | 0.00% | 10.30% | NA |
| Tropical Japonica | 504 | 32.70% | 2.00% | 0.20% | 65.08% | NA |
| Japonica Intermediate | 241 | 71.40% | 2.10% | 0.00% | 26.56% | NA |
| VI/Aromatic | 96 | 31.20% | 19.80% | 0.00% | 48.96% | NA |
| Intermediate | 90 | 37.80% | 21.10% | 1.11% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004377181 | A -> G | LOC_Os10g08080.1 | synonymous_variant ; p.Ser845Ser; LOW | synonymous_codon | Average:22.483; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |
| vg1004377181 | A -> DEL | LOC_Os10g08080.1 | N | frameshift_variant | Average:22.483; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004377181 | NA | 2.47E-07 | mr1090 | 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 |
| vg1004377181 | 6.59E-06 | 2.38E-07 | mr1094 | 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 |
| vg1004377181 | NA | 1.72E-06 | mr1096 | 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 |
| vg1004377181 | NA | 2.24E-06 | mr1068_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 |
| vg1004377181 | 8.86E-07 | 2.04E-09 | mr1090_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 |