| Variant ID: vg0406035761 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 6035761 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCTGTGAAATCGACACACATGCGCCATTTGCCGTTTGACTTCCGCACCAGCACTGGATTCGCCAACCACTCCGTATGGTCAATCTCTTGGATAACCCCC[G/A]
CCCGGAGTAATTTTTGTACTTCGGCCTTCGCCGTTTCTTGGCGAACGCAGACATCTTGCGCAACTTTTGTTTTCTTGGCTTAATATCCGGCTTGACTGCT
AGCAGTCAAGCCGGATATTAAGCCAAGAAAACAAAAGTTGCGCAAGATGTCTGCGTTCGCCAAGAAACGGCGAAGGCCGAAGTACAAAAATTACTCCGGG[C/T]
GGGGGTTATCCAAGAGATTGACCATACGGAGTGGTTGGCGAATCCAGTGCTGGTGCGGAAGTCAAACGGCAAATGGCGCATGTGTGTCGATTTCACAGAT
| 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 | 94.30% | 5.40% | 0.34% | 0.00% | NA |
| All Indica | 2759 | 90.50% | 9.00% | 0.58% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.60% | 5.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 95.10% | 2.60% | 2.37% | 0.00% | NA |
| Indica III | 913 | 86.50% | 13.30% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 89.20% | 10.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0406035761 | G -> A | LOC_Os04g11080.1 | downstream_gene_variant ; 4353.0bp to feature; MODIFIER | silent_mutation | Average:32.986; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| vg0406035761 | G -> A | LOC_Os04g11090.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.986; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0406035761 | NA | 4.36E-06 | mr1246 | 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 |
| vg0406035761 | NA | 4.45E-08 | mr1305 | 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 |
| vg0406035761 | NA | 1.51E-09 | mr1586 | 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 |
| vg0406035761 | NA | 3.83E-07 | mr1765 | 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 |