| Variant ID: vg1013277170 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 13277170 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, G: 0.41, others allele: 0.00, population size: 103. )
GACGACGCCCGAGAGAGAGAGAAGGGGGGAGAGGACAAAGAGGAGGTGAGAGAGAATGACAGGTGGGCCCCCACCATTTAAAAAAAGAAAATGTTGATTA[T/G]
ATCTGCTACTAGTACAAAACCGCTCTAGTTTGGGTTGAGGGGGGTAATTCGTCCGGTCTTGAAAGTTCAGGGTGAGTGATGTCTGGTTTTTGGGTTCATG
CATGAACCCAAAAACCAGACATCACTCACCCTGAACTTTCAAGACCGGACGAATTACCCCCCTCAACCCAAACTAGAGCGGTTTTGTACTAGTAGCAGAT[A/C]
TAATCAACATTTTCTTTTTTTAAATGGTGGGGGCCCACCTGTCATTCTCTCTCACCTCCTCTTTGTCCTCTCCCCCCTTCTCTCTCTCTCGGGCGTCGTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.20% | 21.60% | 0.21% | 0.00% | NA |
| All Indica | 2759 | 74.60% | 25.00% | 0.36% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 1.10% | 98.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 71.10% | 28.20% | 0.67% | 0.00% | NA |
| Indica II | 465 | 93.80% | 5.40% | 0.86% | 0.00% | NA |
| Indica III | 913 | 69.80% | 30.10% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 71.50% | 28.40% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 69.80% | 30.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 21.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1013277170 | T -> G | LOC_Os10g25620.1 | upstream_gene_variant ; 4223.0bp to feature; MODIFIER | silent_mutation | Average:71.089; most accessible tissue: Zhenshan97 young leaf, score: 82.31 | N | N | N | N |
| vg1013277170 | T -> G | LOC_Os10g25630.1 | downstream_gene_variant ; 668.0bp to feature; MODIFIER | silent_mutation | Average:71.089; most accessible tissue: Zhenshan97 young leaf, score: 82.31 | N | N | N | N |
| vg1013277170 | T -> G | LOC_Os10g25640.1 | downstream_gene_variant ; 2183.0bp to feature; MODIFIER | silent_mutation | Average:71.089; most accessible tissue: Zhenshan97 young leaf, score: 82.31 | N | N | N | N |
| vg1013277170 | T -> G | LOC_Os10g25620-LOC_Os10g25630 | intergenic_region ; MODIFIER | silent_mutation | Average:71.089; most accessible tissue: Zhenshan97 young leaf, score: 82.31 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1013277170 | 1.55E-12 | NA | mr1533 | 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 |
| vg1013277170 | 2.25E-14 | 1.98E-20 | mr1533 | 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 |
| vg1013277170 | 8.99E-13 | NA | mr1980 | 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 |
| vg1013277170 | 1.15E-14 | 9.37E-21 | mr1980 | 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 |
| vg1013277170 | 3.50E-13 | NA | mr1533_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 |
| vg1013277170 | 3.92E-15 | 1.41E-25 | mr1533_2 | 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 |
| vg1013277170 | 5.66E-06 | 5.97E-10 | mr1980_2 | 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 |
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