| Variant ID: vg0114587589 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14587589 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 268. )
TACTCACATATGTCAACGTCATTTACCTAGACAAATTTGAAGAATTCAGCAGAAGAAAGATTATGTTCTTGGTTTTCCATAGTCCACATCATGGTCCACA[T/A]
TTGGAGGGAAAATGAAAATTGAGACAGTACCGAGTAGATATCTCCATATATTTGTACCTCTGAAGAGAACAATCCCTGATACAAATTACTGATGCAAAAA
TTTTTGCATCAGTAATTTGTATCAGGGATTGTTCTCTTCAGAGGTACAAATATATGGAGATATCTACTCGGTACTGTCTCAATTTTCATTTTCCCTCCAA[A/T]
TGTGGACCATGATGTGGACTATGGAAAACCAAGAACATAATCTTTCTTCTGCTGAATTCTTCAAATTTGTCTAGGTAAATGACGTTGACATATGTGAGTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.00% | 4.30% | 0.61% | 17.10% | NA |
| All Indica | 2759 | 62.70% | 7.30% | 1.01% | 28.92% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 25.50% | 25.00% | 1.34% | 48.07% | NA |
| Indica II | 465 | 69.50% | 3.00% | 0.22% | 27.31% | NA |
| Indica III | 913 | 78.90% | 0.10% | 1.31% | 19.72% | NA |
| Indica Intermediate | 786 | 68.20% | 4.80% | 0.89% | 26.08% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 1.11% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587589 | T -> A | LOC_Os01g25740.1 | missense_variant ; p.Asn1355Ile; MODERATE | nonsynonymous_codon | Average:63.028; most accessible tissue: Zhenshan97 young leaf, score: 81.102 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0114587589 | T -> DEL | LOC_Os01g25740.1 | N | frameshift_variant | Average:63.028; most accessible tissue: Zhenshan97 young leaf, score: 81.102 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114587589 | NA | 1.19E-06 | mr1519 | 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 |
| vg0114587589 | 8.73E-06 | NA | mr1519_2 | 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 |
| vg0114587589 | 1.87E-06 | 6.16E-10 | mr1519_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 |