Variant ID: vg0316103102 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 16103102 |
Reference Allele: A | Alternative Allele: G,T |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 222. )
CCAACATTCTAGAACCAAGCATATTGACATACGCTATCACTTCCTAAAAGACCATGTTGTTGCCAAGAGTGACATAGTCATTAGCCACATAAGAACCGAG[A/G,T]
ATCAACTAGCCGACATATTTACCAAGCCTCTTGATGAAACCCGCTTTTGCAAGTTGAGAAATGAGTTAAATGTCATAGACTTCTCTAATGTGGCTTGAGA
TCTCAAGCCACATTAGAGAAGTCTATGACATTTAACTCATTTCTCAACTTGCAAAAGCGGGTTTCATCAAGAGGCTTGGTAAATATGTCGGCTAGTTGAT[T/C,A]
CTCGGTTCTTATGTGGCTAATGACTATGTCACTCTTGGCAACAACATGGTCTTTTAGGAAGTGATAGCGTATGTCAATATGCTTGGTTCTAGAATGTTGG
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 | 70.10% | 29.80% | 0.08% | 0.00% | T: 0.02% |
All Indica | 2759 | 98.70% | 1.30% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 19.20% | 80.80% | 0.07% | 0.00% | NA |
Aus | 269 | 80.70% | 19.30% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.20% | 0.50% | 0.34% | 0.00% | NA |
Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 52.80% | 47.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 6.60% | 92.90% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 19.80% | 79.20% | 0.00% | 0.00% | T: 1.04% |
Intermediate | 90 | 72.20% | 26.70% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0316103102 | A -> T | LOC_Os03g28010.1 | missense_variant ; p.Asn1944Tyr; MODERATE | nonsynonymous_codon | Average:28.995; most accessible tissue: Zhenshan97 panicle, score: 39.652 | benign | 0.117 | DELETERIOUS | 0.00 |
vg0316103102 | A -> G | LOC_Os03g28010.1 | missense_variant ; p.Asn1944Asp; MODERATE | nonsynonymous_codon | Average:28.995; most accessible tissue: Zhenshan97 panicle, score: 39.652 | benign | -0.11 | TOLERATED | 1.00 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0316103102 | NA | 8.71E-12 | mr1940 | 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 |
vg0316103102 | 2.25E-06 | NA | mr1676_2 | 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 |