Search for Variation information by Variation ID:
Detailed information for vg0623284811:
| Variant ID: vg0623284811 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 23284811 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 104. )
Flanking Sequence (100 bp) in Reference Genome:
TCTAGAACCATCATTGTGGGAAGGGTTCTCAGGTGGGATGATAGCAATGGGCTCATGCACACAACACACAGAAGCAACATCCATGCTTTCCTCAAGAACT[G/A]
CTACAAGTAAGTGGAAACTGGCCTCGGTTGCATACATCTCGAAAATATCTGGCAAATCAGTGTCCCCTATGAGCCTAACATCCTCACCCAAATTTTTGTT
Reverse complement sequence
AACAAAAATTTGGGTGAGGATGTTAGGCTCATAGGGGACACTGATTTGCCAGATATTTTCGAGATGTATGCAACCGAGGCCAGTTTCCACTTACTTGTAG[C/T]
AGTTCTTGAGGAAAGCATGGATGTTGCTTCTGTGTGTTGTGTGCATGAGCCCATTGCTATCATCCCACCTGAGAACCCTTCCCACAATGATGGTTCTAGA
Allele Frequencies:
| 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 | 40.60% | 1.30% | 18.56% | 39.48% | NA |
| All Indica | 2759 | 10.00% | 2.00% | 28.52% | 59.41% | NA |
| All Japonica | 1512 | 98.40% | 0.00% | 0.26% | 1.32% | NA |
| Aus | 269 | 4.80% | 1.90% | 26.39% | 66.91% | NA |
| Indica I | 595 | 8.70% | 1.70% | 30.92% | 58.66% | NA |
| Indica II | 465 | 14.60% | 2.20% | 20.00% | 63.23% | NA |
| Indica III | 913 | 6.60% | 1.60% | 32.09% | 59.69% | NA |
| Indica Intermediate | 786 | 12.30% | 2.70% | 27.61% | 57.38% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.26% | 1.56% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 4.17% | 5.21% | NA |
| Intermediate | 90 | 62.20% | 1.10% | 12.22% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0623284811 | G -> A | LOC_Os06g39220.1 | missense_variant ; p.Ala127Val; MODERATE | nonsynonymous_codon ; A127V | Average:41.486; most accessible tissue: Minghui63 flag leaf, score: 57.881 | benign  |
0.148 |
TOLERATED | 0.12 |
| vg0623284811 | G -> DEL | LOC_Os06g39220.1 | N | frameshift_variant | Average:41.486; most accessible tissue: Minghui63 flag leaf, score: 57.881 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0623284811 | 4.65E-06 | 4.65E-06 | mr1455 | 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 |