| Variant ID: vg0707015142 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 7015142 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTTGGTACATCTTCGTACTTCCTGGATGAATGGAGTAGGCGGACTCATGAGCTTCCTTTAGGATGAGATCTCTTAATTCCTTCTTGGCCGGTACACAGAT[A/G]
CGTGGACCGCACCAAACTGTGCCTTGATCGTCTATGGAGAAATTGGTGTCTTTCTTCTCCTGTATTCTTTTTATTAACTCTTTTATCCCTTCGTCGTCTT
AAGACGACGAAGGGATAAAAGAGTTAATAAAAAGAATACAGGAGAAGAAAGACACCAATTTCTCCATAGACGATCAAGGCACAGTTTGGTGCGGTCCACG[T/C]
ATCTGTGTACCGGCCAAGAAGGAATTAAGAGATCTCATCCTAAAGGAAGCTCATGAGTCCGCCTACTCCATTCATCCAGGAAGTACGAAGATGTACCAAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.90% | 3.60% | 16.40% | 43.17% | NA |
| All Indica | 2759 | 4.20% | 0.10% | 26.86% | 68.79% | NA |
| All Japonica | 1512 | 88.60% | 10.80% | 0.00% | 0.66% | NA |
| Aus | 269 | 58.70% | 0.00% | 8.92% | 32.34% | NA |
| Indica I | 595 | 2.00% | 0.00% | 45.88% | 52.10% | NA |
| Indica II | 465 | 8.20% | 0.00% | 15.05% | 76.77% | NA |
| Indica III | 913 | 2.10% | 0.10% | 23.11% | 74.70% | NA |
| Indica Intermediate | 786 | 6.10% | 0.30% | 23.79% | 69.85% | NA |
| Temperate Japonica | 767 | 96.90% | 2.70% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 92.50% | 6.70% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 53.90% | 44.80% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 1.04% | 13.54% | NA |
| Intermediate | 90 | 51.10% | 3.30% | 10.00% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0707015142 | A -> DEL | LOC_Os07g12360.1 | N | frameshift_variant | Average:6.736; most accessible tissue: Callus, score: 12.394 | N | N | N | N |
| vg0707015142 | A -> G | LOC_Os07g12360.1 | synonymous_variant ; p.Arg1329Arg; LOW | synonymous_codon | Average:6.736; most accessible tissue: Callus, score: 12.394 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0707015142 | 2.59E-06 | 2.00E-06 | mr1376 | 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 |
| vg0707015142 | 2.59E-06 | 2.00E-06 | mr1431 | 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 |