| Variant ID: vg1004654280 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4654280 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 85. )
AGCGCGCCTGAAGAGGGAGAATGCTCAGTTAAAGGGTCTTCCCGCGCCAGGAGGAGACGTGGATCTGAATGTCAACATTGTCGTCTGTGTACCCCGGCCG[G/A]
TCCTGGACGGGGATTTTAATGCACATTCTGCTTGGAATTCTATTCGGGAATTTCTGGGCGTGGCACCGAACCTATATAAAAATCCATGTCTCCATCTCTT
AAGAGATGGAGACATGGATTTTTATATAGGTTCGGTGCCACGCCCAGAAATTCCCGAATAGAATTCCAAGCAGAATGTGCATTAAAATCCCCGTCCAGGA[C/T]
CGGCCGGGGTACACAGACGACAATGTTGACATTCAGATCCACGTCTCCTCCTGGCGCGGGAAGACCCTTTAACTGAGCATTCTCCCTCTTCAGGCGCGCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.60% | 22.90% | 12.44% | 3.98% | NA |
| All Indica | 2759 | 56.80% | 33.00% | 8.84% | 1.38% | NA |
| All Japonica | 1512 | 62.40% | 10.00% | 18.58% | 8.99% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 60.30% | 39.30% | 0.34% | 0.00% | NA |
| Indica II | 465 | 66.20% | 20.60% | 8.39% | 4.73% | NA |
| Indica III | 913 | 45.50% | 37.30% | 16.76% | 0.44% | NA |
| Indica Intermediate | 786 | 61.70% | 30.40% | 6.36% | 1.53% | NA |
| Temperate Japonica | 767 | 88.90% | 5.20% | 4.17% | 1.69% | NA |
| Tropical Japonica | 504 | 28.40% | 18.30% | 36.11% | 17.26% | NA |
| Japonica Intermediate | 241 | 49.40% | 7.90% | 27.80% | 14.94% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 50.00% | 12.50% | NA |
| Intermediate | 90 | 58.90% | 22.20% | 16.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004654280 | G -> A | LOC_Os10g08560.1 | missense_variant ; p.Val200Ile; MODERATE | nonsynonymous_codon ; V200I | Average:56.193; most accessible tissue: Zhenshan97 flag leaf, score: 85.88 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1004654280 | G -> DEL | LOC_Os10g08560.1 | N | frameshift_variant | Average:56.193; most accessible tissue: Zhenshan97 flag leaf, score: 85.88 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004654280 | 3.83E-06 | 3.12E-07 | mr1415_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 |
| vg1004654280 | 7.57E-06 | 7.56E-06 | mr1424_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 |
| vg1004654280 | 6.44E-06 | 6.44E-06 | mr1562_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 |