| Variant ID: vg0512238377 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12238377 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGGTGAGGGTTACTTTTCTATTGGCACAGTCTATCACACCTTTATATCTGGCTAACCAGTCCATGCCTAGGATGACATCGAGGTCTTTGGATTCTAACA[G/A]
AATAAGGTTGGCTAGAAATGGAACACCTTGAATCTCTATTCTGACAGAGGGGCTAAGTTGTGGATAGAGTGCTTGGTTACTGGGGTACTAACCATCAAAG
CTTTGATGGTTAGTACCCCAGTAACCAAGCACTCTATCCACAACTTAGCCCCTCTGTCAGAATAGAGATTCAAGGTGTTCCATTTCTAGCCAACCTTATT[C/T]
TGTTAGAATCCAAAGACCTCGATGTCATCCTAGGCATGGACTGGTTAGCCAGATATAAAGGTGTGATAGACTGTGCCAATAGAAAAGTAACCCTCACCAG
| 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 | 90.80% | 8.30% | 0.89% | 0.00% | NA |
| All Indica | 2759 | 85.30% | 13.40% | 1.30% | 0.00% | NA |
| All Japonica | 1512 | 99.00% | 0.90% | 0.13% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.10% | 0.37% | 0.00% | NA |
| Indica I | 595 | 84.00% | 15.00% | 1.01% | 0.00% | NA |
| Indica II | 465 | 85.20% | 14.20% | 0.65% | 0.00% | NA |
| Indica III | 913 | 84.70% | 13.60% | 1.75% | 0.00% | NA |
| Indica Intermediate | 786 | 87.00% | 11.60% | 1.40% | 0.00% | NA |
| Temperate Japonica | 767 | 98.80% | 1.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0512238377 | G -> A | LOC_Os05g20840.1 | synonymous_variant ; p.Leu447Leu; LOW | synonymous_codon | Average:57.57; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0512238377 | 2.73E-06 | NA | mr1518 | 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 |
| vg0512238377 | 7.53E-06 | NA | mr1676 | 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 |