| Variant ID: vg1209154479 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9154479 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.59, C: 0.41, others allele: 0.00, population size: 66. )
TGCACTAGAGTCAATCATGAATGTATCTTACGCCCATTGCCCTAGTGTGTGCCTGATGCTTAGGTTGAGGGAGTGGCTTTGTCAACGGATCTGCAACATT[G/C]
AAATCCGTATGTATTTTGCATATCTTCACAACTCCTCTTCCCACTATCTCGCGAATGAGGTGATACCGCCATAAAATGTTGGACTTTTGATGCGATCTAG
CTAGATCGCATCAAAAGTCCAACATTTTATGGCGGTATCACCTCATTCGCGAGATAGTGGGAAGAGGAGTTGTGAAGATATGCAAAATACATACGGATTT[C/G]
AATGTTGCAGATCCGTTGACAAAGCCACTCCCTCAACCTAAGCATCAGGCACACACTAGGGCAATGGGCGTAAGATACATTCATGATTGACTCTAGTGCA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.20% | 5.00% | 2.94% | 57.85% | NA |
| All Indica | 2759 | 3.80% | 6.30% | 3.12% | 86.81% | NA |
| All Japonica | 1512 | 94.30% | 3.20% | 0.20% | 2.31% | NA |
| Aus | 269 | 4.50% | 2.60% | 8.18% | 84.76% | NA |
| Indica I | 595 | 2.50% | 0.30% | 2.18% | 94.96% | NA |
| Indica II | 465 | 4.50% | 12.50% | 2.15% | 80.86% | NA |
| Indica III | 913 | 3.60% | 4.60% | 3.40% | 88.39% | NA |
| Indica Intermediate | 786 | 4.60% | 9.00% | 4.07% | 82.32% | NA |
| Temperate Japonica | 767 | 92.60% | 5.90% | 0.26% | 1.30% | NA |
| Tropical Japonica | 504 | 95.60% | 0.60% | 0.20% | 3.57% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 28.12% | 46.88% | NA |
| Intermediate | 90 | 56.70% | 7.80% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209154479 | G -> C | LOC_Os12g16060.1 | missense_variant ; p.Phe1021Leu; MODERATE | nonsynonymous_codon ; F1021L | Average:8.245; most accessible tissue: Callus, score: 29.89 | unknown | unknown | TOLERATED | 1.00 |
| vg1209154479 | G -> DEL | LOC_Os12g16060.1 | N | frameshift_variant | Average:8.245; most accessible tissue: Callus, score: 29.89 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209154479 | 1.24E-06 | NA | mr1059 | 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 |
| vg1209154479 | 3.03E-06 | NA | mr1167 | 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 |
| vg1209154479 | 2.64E-06 | NA | mr1535 | 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 |
| vg1209154479 | 4.48E-06 | NA | mr1167_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 |