Search for Variation information by Variation ID:
Detailed information for vg1000218960:
| Variant ID: vg1000218960 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 218960 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 109. )
Flanking Sequence (100 bp) in Reference Genome:
GGAGGTTTATGTCCGAACTTGCCGACTAGGTCCTCGTGGCGAATGCCTTTAGTAAAGGCGGCGATGATGACGTCGTCGGTGATGTTGGAGATCTTGTTGC[A/G]
TTGCTCGGAGAAGCGTCGGATGTAATCTCGAAGGGATTCTCCAGACTTCTGAACGACGTTGTAGAGATCAAACTGTGTGCCGGGGCATTCAAAGGTGCCC
Reverse complement sequence
GGGCACCTTTGAATGCCCCGGCACACAGTTTGATCTCTACAACGTCGTTCAGAAGTCTGGAGAATCCCTTCGAGATTACATCCGACGCTTCTCCGAGCAA[T/C]
GCAACAAGATCTCCAACATCACCGACGACGTCATCATCGCCGCCTTTACTAAAGGCATTCGCCACGAGGACCTAGTCGGCAAGTTCGGACATAAACCTCC
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 | 19.10% | 18.10% | 7.58% | 55.14% | NA |
| All Indica | 2759 | 1.70% | 28.70% | 12.21% | 57.38% | NA |
| All Japonica | 1512 | 54.00% | 2.30% | 0.33% | 43.39% | NA |
| Aus | 269 | 4.10% | 5.20% | 2.23% | 88.48% | NA |
| Indica I | 595 | 2.90% | 18.50% | 13.11% | 65.55% | NA |
| Indica II | 465 | 1.70% | 46.70% | 8.17% | 43.44% | NA |
| Indica III | 913 | 0.70% | 23.40% | 14.68% | 61.23% | NA |
| Indica Intermediate | 786 | 1.90% | 32.10% | 11.07% | 54.96% | NA |
| Temperate Japonica | 767 | 84.60% | 2.20% | 0.26% | 12.91% | NA |
| Tropical Japonica | 504 | 9.30% | 2.40% | 0.60% | 87.70% | NA |
| Japonica Intermediate | 241 | 49.80% | 2.50% | 0.00% | 47.72% | NA |
| VI/Aromatic | 96 | 10.40% | 1.00% | 4.17% | 84.38% | NA |
| Intermediate | 90 | 24.40% | 15.60% | 6.67% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000218960 | A -> G | LOC_Os10g01360.1 | missense_variant ; p.Cys454Arg; MODERATE | nonsynonymous_codon ; C454R | Average:20.234; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | benign  |
-0.476 |
TOLERATED | 1.00 |
| vg1000218960 | A -> DEL | LOC_Os10g01360.1 | N | frameshift_variant | Average:20.234; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000218960 | NA | 4.35E-06 | mr1195 | 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 |
| vg1000218960 | 2.87E-06 | 2.87E-06 | mr1644 | 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 |
| vg1000218960 | NA | 8.69E-07 | mr1709 | 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 |
| vg1000218960 | NA | 6.35E-06 | mr1158_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 |
| vg1000218960 | NA | 8.10E-06 | mr1613_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 |