| Variant ID: vg1000028876 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 28876 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAAGTCGAAGTCGGAAGGCAACCCGGCAAAAGGATCCTCAATCTCTTCATCCTCTGGCTCATCGGGCTCGGCCTCGAAACCTGGAGGAGAAGGAGGGATA[T/G]
CAATGTGGTGGTCCTCATAATACCTTGCCTTGAGGAACTTGACATCACGAGCCGTTTTCTTTGCCGAATTCCGCAATCGGTGGTTCTTTTTGGCCTCCGT
ACGGAGGCCAAAAAGAACCACCGATTGCGGAATTCGGCAAAGAAAACGGCTCGTGATGTCAAGTTCCTCAAGGCAAGGTATTATGAGGACCACCACATTG[A/C]
TATCCCTCCTTCTCCTCCAGGTTTCGAGGCCGAGCCCGATGAGCCAGAGGATGAAGAGATTGAGGATCCTTTTGCCGGGTTGCCTTCCGACTTCGACTTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.80% | 2.20% | 21.75% | 40.27% | NA |
| All Indica | 2759 | 13.50% | 3.00% | 33.49% | 49.98% | NA |
| All Japonica | 1512 | 70.20% | 1.40% | 2.38% | 26.06% | NA |
| Aus | 269 | 62.80% | 0.00% | 19.70% | 17.47% | NA |
| Indica I | 595 | 8.10% | 0.30% | 18.99% | 72.61% | NA |
| Indica II | 465 | 9.50% | 5.40% | 27.96% | 57.20% | NA |
| Indica III | 913 | 13.90% | 4.90% | 48.30% | 32.86% | NA |
| Indica Intermediate | 786 | 19.50% | 1.50% | 30.53% | 48.47% | NA |
| Temperate Japonica | 767 | 90.40% | 0.00% | 0.65% | 9.00% | NA |
| Tropical Japonica | 504 | 42.10% | 4.20% | 4.96% | 48.81% | NA |
| Japonica Intermediate | 241 | 64.70% | 0.00% | 2.49% | 32.78% | NA |
| VI/Aromatic | 96 | 43.80% | 0.00% | 5.21% | 51.04% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 11.11% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000028876 | T -> G | LOC_Os10g01020.1 | missense_variant ; p.Asp1930Ala; MODERATE | nonsynonymous_codon ; D1930A | Average:12.251; most accessible tissue: Callus, score: 29.075 | unknown | unknown | TOLERATED | 0.32 |
| vg1000028876 | T -> DEL | LOC_Os10g01020.1 | N | frameshift_variant | Average:12.251; most accessible tissue: Callus, score: 29.075 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000028876 | 1.13E-06 | 4.37E-06 | mr1550 | 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 |
| vg1000028876 | 3.41E-06 | 3.41E-06 | mr1823 | 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 |