| Variant ID: vg1011360991 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 11360991 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCAAAAAGAAAGGACTCGTCGACATCGCCCGCGTTTTCAGCGACGATGAGTCTTCTGACGAGACTCCGACCTCGCCTGCTGGCCGCAGTTTGGACCTCTC[G/A]
ACTGCTCCCCTTGCTCCGCTCGGCGTTGCTGGTGCAGGCGGTAGTGCCGCCGCCAGGGCTTCCGCCTCCGCCAAACGGATCGTGTCGGCCGCGGCGATGG
CCATCGCCGCGGCCGACACGATCCGTTTGGCGGAGGCGGAAGCCCTGGCGGCGGCACTACCGCCTGCACCAGCAACGCCGAGCGGAGCAAGGGGAGCAGT[C/T]
GAGAGGTCCAAACTGCGGCCAGCAGGCGAGGTCGGAGTCTCGTCAGAAGACTCATCGTCGCTGAAAACGCGGGCGATGTCGACGAGTCCTTTCTTTTTGG
| 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 | 60.10% | 3.60% | 13.58% | 22.70% | NA |
| All Indica | 2759 | 64.80% | 2.20% | 19.14% | 13.88% | NA |
| All Japonica | 1512 | 41.80% | 7.10% | 6.22% | 44.91% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 50.40% | 1.30% | 22.86% | 25.38% | NA |
| Indica II | 465 | 58.70% | 2.40% | 24.52% | 14.41% | NA |
| Indica III | 913 | 76.10% | 2.40% | 14.90% | 6.57% | NA |
| Indica Intermediate | 786 | 66.20% | 2.40% | 18.07% | 13.36% | NA |
| Temperate Japonica | 767 | 71.80% | 1.30% | 1.17% | 25.68% | NA |
| Tropical Japonica | 504 | 7.10% | 17.30% | 12.30% | 63.29% | NA |
| Japonica Intermediate | 241 | 18.70% | 4.10% | 9.54% | 67.63% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 63.30% | 4.40% | 21.11% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1011360991 | G -> A | LOC_Os10g22000.1 | synonymous_variant ; p.Ser448Ser; LOW | synonymous_codon | Average:36.899; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| vg1011360991 | G -> DEL | LOC_Os10g22000.1 | N | frameshift_variant | Average:36.899; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1011360991 | 5.42E-07 | NA | mr1805 | 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 |
| vg1011360991 | 3.88E-06 | 1.09E-06 | mr1805 | 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 |