| Variant ID: vg0710453841 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10453841 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGTTTCCACGTGTGCAGGCCGTGTGGTGTCTCGTGGAGTCCTTTTGTCGGCCACTCGCCTCAGTTGACACACGGGATCCGCTTCCGTCGACCCGTGGACC[G/A]
TCTCTGTGTACTTGGTCTACTGTGGTCCCTTAGGTTGACTTGTGGGGTCCACATGTCAACGGCGCAGCCTTCTTGTCTTTTCCAGGCTAGCGCTTATATA
TATATAAGCGCTAGCCTGGAAAAGACAAGAAGGCTGCGCCGTTGACATGTGGACCCCACAAGTCAACCTAAGGGACCACAGTAGACCAAGTACACAGAGA[C/T]
GGTCCACGGGTCGACGGAAGCGGATCCCGTGTGTCAACTGAGGCGAGTGGCCGACAAAAGGACTCCACGAGACACCACACGGCCTGCACACGTGGAAACC
| 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 | 52.30% | 21.10% | 25.14% | 1.46% | NA |
| All Indica | 2759 | 32.00% | 32.20% | 35.56% | 0.25% | NA |
| All Japonica | 1512 | 88.80% | 1.60% | 8.07% | 1.59% | NA |
| Aus | 269 | 61.00% | 17.80% | 20.45% | 0.74% | NA |
| Indica I | 595 | 35.00% | 26.90% | 38.15% | 0.00% | NA |
| Indica II | 465 | 18.50% | 42.60% | 38.92% | 0.00% | NA |
| Indica III | 913 | 31.90% | 34.80% | 32.86% | 0.44% | NA |
| Indica Intermediate | 786 | 37.90% | 27.00% | 34.73% | 0.38% | NA |
| Temperate Japonica | 767 | 83.20% | 2.70% | 14.08% | 0.00% | NA |
| Tropical Japonica | 504 | 93.10% | 0.20% | 2.58% | 4.17% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.80% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 38.50% | 13.50% | 14.58% | 33.33% | NA |
| Intermediate | 90 | 53.30% | 24.40% | 17.78% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710453841 | G -> DEL | N | N | silent_mutation | Average:27.342; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
| vg0710453841 | G -> A | LOC_Os07g17700.1 | downstream_gene_variant ; 1887.0bp to feature; MODIFIER | silent_mutation | Average:27.342; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
| vg0710453841 | G -> A | LOC_Os07g17710.1 | downstream_gene_variant ; 4379.0bp to feature; MODIFIER | silent_mutation | Average:27.342; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
| vg0710453841 | G -> A | LOC_Os07g17700-LOC_Os07g17710 | intergenic_region ; MODIFIER | silent_mutation | Average:27.342; most accessible tissue: Zhenshan97 flag leaf, score: 48.165 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0710453841 | NA | 2.78E-06 | mr1028 | 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 |
| vg0710453841 | NA | 7.03E-06 | mr1453 | 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 |
| vg0710453841 | NA | 2.21E-07 | mr1652 | 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 |
| vg0710453841 | 4.63E-06 | NA | mr1599_2 | 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 |