| Variant ID: vg0601078672 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 1078672 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, T: 0.42, others allele: 0.00, population size: 59. )
GTGACGGCCATGGTTTCCCCACGGGATAGCCTCCTCACGAAGTAGTCGCCGACCTCCGCCTCCGGGTTGGTCGTCCACTGCGTCGTCACCACCTGCATCA[T/C]
CTTCCCCGGCTGCAAGTCCGTGATGTTGGGCAAGTAGAAGAGGTTAGCCATGCTGATCACGCCGCCGCCGGAGACGGAGACGGCCAAGACGGCGACGGAC
GTCCGTCGCCGTCTTGGCCGTCTCCGTCTCCGGCGGCGGCGTGATCAGCATGGCTAACCTCTTCTACTTGCCCAACATCACGGACTTGCAGCCGGGGAAG[A/G]
TGATGCAGGTGGTGACGACGCAGTGGACGACCAACCCGGAGGCGGAGGTCGGCGACTACTTCGTGAGGAGGCTATCCCGTGGGGAAACCATGGCCGTCAC
| 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 | 55.10% | 12.70% | 0.93% | 31.27% | NA |
| All Indica | 2759 | 41.80% | 11.80% | 1.20% | 45.20% | NA |
| All Japonica | 1512 | 90.30% | 3.90% | 0.66% | 5.16% | NA |
| Aus | 269 | 8.20% | 41.60% | 0.00% | 50.19% | NA |
| Indica I | 595 | 69.90% | 5.50% | 0.17% | 24.37% | NA |
| Indica II | 465 | 60.90% | 5.20% | 1.94% | 32.04% | NA |
| Indica III | 913 | 14.10% | 19.30% | 1.20% | 65.39% | NA |
| Indica Intermediate | 786 | 41.30% | 11.80% | 1.53% | 45.29% | NA |
| Temperate Japonica | 767 | 92.60% | 6.50% | 0.78% | 0.13% | NA |
| Tropical Japonica | 504 | 84.50% | 0.40% | 0.79% | 14.29% | NA |
| Japonica Intermediate | 241 | 95.00% | 2.90% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 4.20% | 94.80% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 64.40% | 15.60% | 1.11% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0601078672 | T -> C | LOC_Os06g02930.1 | missense_variant ; p.Met128Val; MODERATE | nonsynonymous_codon ; M128V | Average:74.29; most accessible tissue: Minghui63 young leaf, score: 83.907 | unknown | unknown | TOLERATED | 1.00 |
| vg0601078672 | T -> DEL | LOC_Os06g02930.1 | N | frameshift_variant | Average:74.29; most accessible tissue: Minghui63 young leaf, score: 83.907 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0601078672 | 2.53E-06 | 9.62E-06 | mr1137 | 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 |
| vg0601078672 | 6.18E-07 | 2.35E-06 | mr1519 | 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 |
| vg0601078672 | NA | 9.75E-08 | mr1585_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 |