Search for Variation information by Variation ID:
Detailed information for vg1003367906:
| Variant ID: vg1003367906 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 3367906 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 101. )
Flanking Sequence (100 bp) in Reference Genome:
GCCGTCGATCCTAGTAATGTGGAATCCGTAACCAACTGGAAACAACCAAAGACAGTTTCAGAGATCCGCAGTTTCCTAGGCCTCGCAGGATATTATCGGA[A/G]
GTTTATAGAGAATTTTTCCAAGATTGCTAAGCCCATGACACGACTGTTTCAGAAAGATGTGAAGTACAAGTGGTCAGAAGAATGTGAGCAGAGTTTTCAA
Reverse complement sequence
TTGAAAACTCTGCTCACATTCTTCTGACCACTTGTACTTCACATCTTTCTGAAACAGTCGTGTCATGGGCTTAGCAATCTTGGAAAAATTCTCTATAAAC[T/C]
TCCGATAATATCCTGCGAGGCCTAGGAAACTGCGGATCTCTGAAACTGTCTTTGGTTGTTTCCAGTTGGTTACGGATTCCACATTACTAGGATCGACGGC
Allele Frequencies:
| 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 | 36.90% | 6.00% | 47.19% | 9.84% | NA |
| All Indica | 2759 | 13.50% | 9.60% | 67.09% | 9.82% | NA |
| All Japonica | 1512 | 81.90% | 0.10% | 5.49% | 12.57% | NA |
| Aus | 269 | 9.70% | 3.30% | 86.62% | 0.37% | NA |
| Indica I | 595 | 15.80% | 8.60% | 61.34% | 14.29% | NA |
| Indica II | 465 | 7.50% | 8.80% | 75.48% | 8.17% | NA |
| Indica III | 913 | 16.10% | 10.60% | 62.87% | 10.41% | NA |
| Indica Intermediate | 786 | 12.20% | 9.70% | 71.37% | 6.74% | NA |
| Temperate Japonica | 767 | 71.10% | 0.10% | 4.82% | 23.99% | NA |
| Tropical Japonica | 504 | 95.00% | 0.00% | 4.96% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 8.71% | 2.49% | NA |
| VI/Aromatic | 96 | 66.70% | 4.20% | 29.17% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 6.70% | 38.89% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1003367906 | A -> G | LOC_Os10g06550.1 | missense_variant ; p.Lys967Arg; MODERATE | nonsynonymous_codon ; K967R | Average:28.677; most accessible tissue: Minghui63 young leaf, score: 45.896 | benign  |
-1.366 |
TOLERATED | 1.00 |
| vg1003367906 | A -> DEL | LOC_Os10g06550.1 | N | frameshift_variant | Average:28.677; most accessible tissue: Minghui63 young leaf, score: 45.896 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1003367906 | NA | 7.96E-06 | mr1305 | 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 |
| vg1003367906 | 5.21E-08 | 1.01E-08 | mr1310 | 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 |
| vg1003367906 | NA | 3.81E-12 | mr1666_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 |
| vg1003367906 | 1.10E-09 | 7.25E-17 | mr1709_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 |
| vg1003367906 | NA | 1.33E-11 | mr1761_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 |