| Variant ID: vg0400024076 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24076 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATTATATAGGAATTTAAACTGCAATTGTTCTGATCTGAATTAAAACACTTAAAAAGCAAGCAAAAATCCTTATTAAGACAACCATATCATAGGCACATGA[T/C]
ATCGACCGTCGACTGACCCACGAGCAAGCAACCTAAACACACAAACTAACAAACAAATGCTAGACAGTCGATAAACTAATGGAAAACGAGCCTAATGCTT
AAGCATTAGGCTCGTTTTCCATTAGTTTATCGACTGTCTAGCATTTGTTTGTTAGTTTGTGTGTTTAGGTTGCTTGCTCGTGGGTCAGTCGACGGTCGAT[A/G]
TCATGTGCCTATGATATGGTTGTCTTAATAAGGATTTTTGCTTGCTTTTTAAGTGTTTTAATTCAGATCAGAACAATTGCAGTTTAAATTCCTATATAAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.50% | 0.50% | 3.96% | 11.00% | NA |
| All Indica | 2759 | 91.60% | 0.50% | 4.60% | 3.23% | NA |
| All Japonica | 1512 | 70.60% | 0.40% | 2.45% | 26.59% | NA |
| Aus | 269 | 98.90% | 0.40% | 0.74% | 0.00% | NA |
| Indica I | 595 | 95.10% | 0.50% | 3.70% | 0.67% | NA |
| Indica II | 465 | 96.30% | 0.90% | 2.15% | 0.65% | NA |
| Indica III | 913 | 92.70% | 0.50% | 4.82% | 1.97% | NA |
| Indica Intermediate | 786 | 85.00% | 0.40% | 6.49% | 8.14% | NA |
| Temperate Japonica | 767 | 79.30% | 0.00% | 1.56% | 19.17% | NA |
| Tropical Japonica | 504 | 62.50% | 0.80% | 3.97% | 32.74% | NA |
| Japonica Intermediate | 241 | 59.80% | 0.80% | 2.07% | 37.34% | NA |
| VI/Aromatic | 96 | 56.20% | 1.00% | 17.71% | 25.00% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 4.44% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0400024076 | T -> C | LOC_Os04g01030.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.4; most accessible tissue: Callus, score: 14.401 | N | N | N | N |
| vg0400024076 | T -> DEL | N | N | silent_mutation | Average:7.4; most accessible tissue: Callus, score: 14.401 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0400024076 | 6.95E-06 | 6.95E-06 | mr1207_2 | 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 |
| vg0400024076 | NA | 6.27E-06 | mr1502_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 |
| vg0400024076 | NA | 4.89E-06 | mr1729_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 |
| vg0400024076 | NA | 6.28E-06 | mr1736_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 |