| Variant ID: vg0309964337 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 9964337 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAGTATACACAGAATGACAATGCCAAATCCAGCCCATATATCAAGGAGAAAAAAACAAATCTAATTCAGAAGGGGAAGTCTTAATTAACCCCTTAAACGA[T/A]
TGGGTGAGTACAGATTATACCTTTTAGACCCAAAAACCATATATCTTTCACCCTCAACCACTGATACCATAGTGGTTTTGTTCTTACGTGGCAGTCCACT
AGTGGACTGCCACGTAAGAACAAAACCACTATGGTATCAGTGGTTGAGGGTGAAAGATATATGGTTTTTGGGTCTAAAAGGTATAATCTGTACTCACCCA[A/T]
TCGTTTAAGGGGTTAATTAAGACTTCCCCTTCTGAATTAGATTTGTTTTTTTCTCCTTGATATATGGGCTGGATTTGGCATTGTCATTCTGTGTATACTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.40% | 3.70% | 0.91% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 86.00% | 11.20% | 2.71% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 97.10% | 0.50% | 2.35% | 0.00% | NA |
| Tropical Japonica | 504 | 80.40% | 17.90% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 62.70% | 31.50% | 5.81% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0309964337 | T -> A | LOC_Os03g17880.1 | upstream_gene_variant ; 2834.0bp to feature; MODIFIER | silent_mutation | Average:82.195; most accessible tissue: Minghui63 flower, score: 89.373 | N | N | N | N |
| vg0309964337 | T -> A | LOC_Os03g17890.1 | upstream_gene_variant ; 1036.0bp to feature; MODIFIER | silent_mutation | Average:82.195; most accessible tissue: Minghui63 flower, score: 89.373 | N | N | N | N |
| vg0309964337 | T -> A | LOC_Os03g17880-LOC_Os03g17890 | intergenic_region ; MODIFIER | silent_mutation | Average:82.195; most accessible tissue: Minghui63 flower, score: 89.373 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0309964337 | NA | 6.91E-07 | mr1114 | 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 |
| vg0309964337 | NA | 5.44E-07 | mr1117 | 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 |
| vg0309964337 | NA | 2.50E-06 | mr1118 | 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 |
| vg0309964337 | NA | 5.16E-06 | mr1119 | 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 |
| vg0309964337 | NA | 4.92E-06 | mr1120 | 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 |
| vg0309964337 | NA | 4.88E-07 | mr1123 | 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 |
| vg0309964337 | NA | 2.12E-07 | mr1180 | 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 |
| vg0309964337 | NA | 9.37E-06 | mr1240 | 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 |
| vg0309964337 | NA | 8.84E-08 | mr1242 | 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 |
| vg0309964337 | NA | 5.36E-06 | mr1247 | 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 |
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