| Variant ID: vg0504908967 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 4908967 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.24, others allele: 0.00, population size: 62. )
TTTATTGCGGATTGCCCTCACCTCAAGGATGGTTCCCACATGAAGGAAGATAAGAAGAAGAGTGAGAAGAAGGATGAGAAGAAGGAGAAGCACAAGCATA[A/G]
CAAGAGGGAACATTATGGCCAAGCTCACCTTGGGATGATCTTCGGCTTCGACTCCGAGTTAAGCTCAAGTGATGAAGAAGGAGTCGCCACGTTCGCTGTC
GACAGCGAACGTGGCGACTCCTTCTTCATCACTTGAGCTTAACTCGGAGTCGAAGCCGAAGATCATCCCAAGGTGAGCTTGGCCATAATGTTCCCTCTTG[T/C]
TATGCTTGTGCTTCTCCTTCTTCTCATCCTTCTTCTCACTCTTCTTCTTATCTTCCTTCATGTGGGAACCATCCTTGAGGTGAGGGCAATCCGCAATAAA
| 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 | 72.80% | 9.80% | 15.85% | 1.54% | NA |
| All Indica | 2759 | 66.90% | 5.60% | 25.08% | 2.39% | NA |
| All Japonica | 1512 | 93.10% | 6.70% | 0.26% | 0.00% | NA |
| Aus | 269 | 7.80% | 73.60% | 16.73% | 1.86% | NA |
| Indica I | 595 | 91.60% | 0.70% | 6.72% | 1.01% | NA |
| Indica II | 465 | 39.40% | 7.10% | 47.10% | 6.45% | NA |
| Indica III | 913 | 65.30% | 6.20% | 27.05% | 1.42% | NA |
| Indica Intermediate | 786 | 66.50% | 7.60% | 23.66% | 2.16% | NA |
| Temperate Japonica | 767 | 97.30% | 2.50% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 88.30% | 11.30% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 4.20% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 7.80% | 5.56% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0504908967 | A -> DEL | LOC_Os05g08880.1 | N | frameshift_variant | Average:30.917; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
| vg0504908967 | A -> G | LOC_Os05g08880.1 | missense_variant ; p.Asn223Ser; MODERATE | nonsynonymous_codon | Average:30.917; most accessible tissue: Zhenshan97 root, score: 62.394 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0504908967 | NA | 5.56E-06 | mr1639 | 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 |
| vg0504908967 | 1.12E-06 | NA | mr1829 | 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 |
| vg0504908967 | NA | 2.41E-06 | mr1546_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 |