| Variant ID: vg0601058374 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 1058374 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.63, G: 0.37, others allele: 0.00, population size: 51. )
GGCAAATAATTTGGCACACCCAACCTATGAGAAACTGGATAGAGTTTTAGTGTCCACGGAATGGGAGCAAAAATACCCTTTATCCTCTGTTGTTGCTCTC[G/A]
ATAGAGATATTTCAGACCATACTCCTTTGCTCCTAAATACAAAATCTTCCTCTTTTAGTAACGCTCAACATAGTTTTAAGTTTGAACTTGGTTGGCTGTT
AACAGCCAACCAAGTTCAAACTTAAAACTATGTTGAGCGTTACTAAAAGAGGAAGATTTTGTATTTAGGAGCAAAGGAGTATGGTCTGAAATATCTCTAT[C/T]
GAGAGCAACAACAGAGGATAAAGGGTATTTTTGCTCCCATTCCGTGGACACTAAAACTCTATCCAGTTTCTCATAGGTTGGGTGTGCCAAATTATTTGCC
| 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 | 50.70% | 35.30% | 2.79% | 11.15% | NA |
| All Indica | 2759 | 35.20% | 47.30% | 4.28% | 13.19% | NA |
| All Japonica | 1512 | 90.00% | 1.30% | 0.26% | 8.40% | NA |
| Aus | 269 | 1.90% | 90.00% | 2.23% | 5.95% | NA |
| Indica I | 595 | 57.30% | 20.70% | 5.21% | 16.81% | NA |
| Indica II | 465 | 55.30% | 28.20% | 7.31% | 9.25% | NA |
| Indica III | 913 | 12.50% | 74.80% | 1.86% | 10.84% | NA |
| Indica Intermediate | 786 | 33.00% | 46.90% | 4.58% | 15.52% | NA |
| Temperate Japonica | 767 | 92.80% | 0.00% | 0.00% | 7.17% | NA |
| Tropical Japonica | 504 | 83.30% | 2.60% | 0.60% | 13.49% | NA |
| Japonica Intermediate | 241 | 95.00% | 2.90% | 0.41% | 1.66% | NA |
| VI/Aromatic | 96 | 4.20% | 83.30% | 1.04% | 11.46% | NA |
| Intermediate | 90 | 62.20% | 24.40% | 3.33% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0601058374 | G -> A | LOC_Os06g02880.1 | missense_variant ; p.Asp249Asn; MODERATE | nonsynonymous_codon ; D249N | Average:32.734; most accessible tissue: Minghui63 panicle, score: 50.413 | unknown | unknown | TOLERATED | 1.00 |
| vg0601058374 | G -> DEL | LOC_Os06g02880.1 | N | frameshift_variant | Average:32.734; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0601058374 | NA | 1.41E-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 |
| vg0601058374 | 3.70E-06 | 8.52E-07 | mr1502 | 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 |