Search for Variation information by Variation ID:
Detailed information for vg0629061910:
| Variant ID: vg0629061910 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29061910 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 336. )
Flanking Sequence (100 bp) in Reference Genome:
GAATGGCCTAAACTAGAGTGTCCATTTAAGCCCCTTGGTCTAGAAGAACTCTCTCCGTCAAATGCCCTGTTTCTCATAACCTCAGCCCTCTTATTATGAA[T/C]
AGAATTAGCTGAAGAACAGCCAGAAGGCAAAACATCAGATATTGATGTGCAGCCAAGGTTTTTTAGAGTACGTCTCTGTACCCCAGGGCCAGCAGCATTT
Reverse complement sequence
AAATGCTGCTGGCCCTGGGGTACAGAGACGTACTCTAAAAAACCTTGGCTGCACATCAATATCTGATGTTTTGCCTTCTGGCTGTTCTTCAGCTAATTCT[A/G]
TTCATAATAAGAGGGCTGAGGTTATGAGAAACAGGGCATTTGACGGAGAGAGTTCTTCTAGACCAAGGGGCTTAAATGGACACTCTAGTTTAGGCCATTC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.50% | 36.40% | 0.00% | 0.11% | NA |
| All Indica | 2759 | 96.20% | 3.60% | 0.00% | 0.14% | NA |
| All Japonica | 1512 | 4.50% | 95.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 47.20% | 52.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.90% | 8.90% | 0.00% | 0.17% | NA |
| Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 3.80% | 0.00% | 0.38% | NA |
| Temperate Japonica | 767 | 3.10% | 96.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 6.70% | 93.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 34.40% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629061910 | T -> C | LOC_Os06g48040.1 | missense_variant ; p.Ile245Val; MODERATE | nonsynonymous_codon ; I245V | Average:73.788; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | benign  |
-0.877 |
TOLERATED | 1.00 |
| vg0629061910 | T -> DEL | LOC_Os06g48040.1 | N | frameshift_variant | Average:73.788; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0629061910 | NA | 3.00E-27 | mr1251 | 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 |
| vg0629061910 | NA | 7.07E-18 | mr1253 | 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 |
| vg0629061910 | NA | 3.81E-36 | mr1435 | 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 |
| vg0629061910 | NA | 8.95E-30 | 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 |
| vg0629061910 | NA | 2.32E-16 | mr1968 | 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 |
| vg0629061910 | NA | 3.45E-57 | mr1064_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 |
| vg0629061910 | NA | 2.14E-36 | mr1129_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 |
| vg0629061910 | NA | 7.30E-22 | mr1253_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 |
| vg0629061910 | NA | 1.09E-06 | mr1321_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 |
| vg0629061910 | NA | 1.66E-10 | mr1349_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 |