| Variant ID: vg1011434213 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 11434213 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCCCAAAACACTGGACAAGAGCCATCGCATTGAGAAACCTTCATTGCATGTCGCTATCACCACCCGGAAAAGATCGAGGTAGCACAACCCTCTTACCAAC[T/C]
GCCAAACCGCTTGTCTCTCCAGAAGAAAGCACGTCAACCACACCCTGCAATCATTAAATAACACTATGATCAAATAACCAGTATGTTGAATCATAGATGG
CCATCTATGATTCAACATACTGGTTATTTGATCATAGTGTTATTTAATGATTGCAGGGTGTGGTTGACGTGCTTTCTTCTGGAGAGACAAGCGGTTTGGC[A/G]
GTTGGTAAGAGGGTTGTGCTACCTCGATCTTTTCCGGGTGGTGATAGCGACATGCAATGAAGGTTTCTCAATGCGATGGCTCTTGTCCAGTGTTTTGGGA
| 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 | 48.50% | 5.60% | 4.08% | 41.83% | NA |
| All Indica | 2759 | 46.10% | 9.30% | 5.94% | 38.71% | NA |
| All Japonica | 1512 | 52.10% | 0.30% | 1.19% | 46.43% | NA |
| Aus | 269 | 50.20% | 0.40% | 1.86% | 47.58% | NA |
| Indica I | 595 | 47.60% | 17.60% | 3.36% | 31.43% | NA |
| Indica II | 465 | 30.50% | 6.20% | 7.10% | 56.13% | NA |
| Indica III | 913 | 53.80% | 7.00% | 5.91% | 33.30% | NA |
| Indica Intermediate | 786 | 45.20% | 7.40% | 7.25% | 40.20% | NA |
| Temperate Japonica | 767 | 77.40% | 0.10% | 0.13% | 22.29% | NA |
| Tropical Japonica | 504 | 26.20% | 0.00% | 2.38% | 71.43% | NA |
| Japonica Intermediate | 241 | 25.70% | 1.20% | 2.07% | 70.95% | NA |
| VI/Aromatic | 96 | 45.80% | 2.10% | 3.12% | 48.96% | NA |
| Intermediate | 90 | 60.00% | 1.10% | 3.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011434213 | T -> C | LOC_Os10g22140.1 | synonymous_variant ; p.Ala602Ala; LOW | synonymous_codon | Average:18.242; most accessible tissue: Callus, score: 51.354 | N | N | N | N |
| vg1011434213 | T -> DEL | LOC_Os10g22140.1 | N | frameshift_variant | Average:18.242; most accessible tissue: Callus, score: 51.354 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011434213 | NA | 5.02E-06 | mr1106 | 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 |
| vg1011434213 | NA | 6.75E-06 | mr1169 | 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 |
| vg1011434213 | NA | 9.68E-06 | mr1229 | 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 |
| vg1011434213 | 2.11E-06 | 1.25E-06 | mr1720 | 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 |