Search for Variation information by Variation ID:
Detailed information for vg1104321369:
| Variant ID: vg1104321369 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 4321369 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 94. )
Flanking Sequence (100 bp) in Reference Genome:
GACCTTGGTGAAAATTTTGAAACTGACATTCAAAAGACATATTGGCCTGTACTGTTGTATATGGTTTGCCTCATGAACTTTTGGAAGAAGTGTAATTATC[T/C]
CAAAATTGAGACTAAACAATGGTAAATCACCCACATGGAAATCCCGGAATAGATTCATCAAATCATCTTTGATGACCTCCCAAAAATTCTGGTAGAACTC
Reverse complement sequence
GAGTTCTACCAGAATTTTTGGGAGGTCATCAAAGATGATTTGATGAATCTATTCCGGGATTTCCATGTGGGTGATTTACCATTGTTTAGTCTCAATTTTG[A/G]
GATAATTACACTTCTTCCAAAAGTTCATGAGGCAAACCATATACAACAGTACAGGCCAATATGTCTTTTGAATGTCAGTTTCAAAATTTTCACCAAGGTC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.90% | 1.00% | 9.86% | 47.21% | NA |
| All Indica | 2759 | 14.00% | 0.80% | 14.24% | 70.97% | NA |
| All Japonica | 1512 | 90.50% | 1.20% | 1.65% | 6.61% | NA |
| Aus | 269 | 64.30% | 0.00% | 15.61% | 20.07% | NA |
| Indica I | 595 | 23.90% | 0.70% | 7.90% | 67.56% | NA |
| Indica II | 465 | 9.20% | 1.10% | 9.03% | 80.65% | NA |
| Indica III | 913 | 9.60% | 0.50% | 20.59% | 69.22% | NA |
| Indica Intermediate | 786 | 14.40% | 1.00% | 14.76% | 69.85% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.52% | 0.65% | NA |
| Tropical Japonica | 504 | 76.80% | 2.60% | 4.17% | 16.47% | NA |
| Japonica Intermediate | 241 | 92.90% | 2.10% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 14.60% | 5.20% | 2.08% | 78.12% | NA |
| Intermediate | 90 | 44.40% | 2.20% | 4.44% | 48.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1104321369 | T -> DEL | LOC_Os11g08230.1 | N | frameshift_variant | Average:15.436; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg1104321369 | T -> C | LOC_Os11g08230.1 | missense_variant ; p.Glu488Gly; MODERATE | nonsynonymous_codon ; E488G | Average:15.436; most accessible tissue: Zhenshan97 panicle, score: 32.308 | benign  |
-0.842 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1104321369 | NA | 2.09E-06 | mr1347 | 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 |
| vg1104321369 | NA | 2.30E-06 | mr1522 | 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 |
| vg1104321369 | NA | 9.47E-06 | mr1571 | 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 |
| vg1104321369 | 1.41E-15 | 2.84E-56 | mr1638 | 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 |
| vg1104321369 | 3.64E-11 | 1.06E-14 | mr1638 | 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 |
| vg1104321369 | NA | 3.79E-06 | mr1963 | 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 |
| vg1104321369 | 1.26E-06 | 1.14E-06 | mr1188_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 |