Variant ID: vg1218153472 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 18153472 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 81. )
TACGTCTCGCCGCTGCCCGGCTCTGTGCCACTAGAACTGCTGCTGCTATGGTCGCGGCTGCCACTAGGAGTAGCAGGTAACCAACCTCCGTTGCCACCGG[T/C]
TGGCCCCCTGACGGCTGACGCTGGAGCGAAGGAGAGAGCGGATGCGGGAGCTGACACTGGAGCAGGAGCTGGGGCTGGAGCTAGAGCTGCGGGCACTGCA
TGCAGTGCCCGCAGCTCTAGCTCCAGCCCCAGCTCCTGCTCCAGTGTCAGCTCCCGCATCCGCTCTCTCCTTCGCTCCAGCGTCAGCCGTCAGGGGGCCA[A/G]
CCGGTGGCAACGGAGGTTGGTTACCTGCTACTCCTAGTGGCAGCCGCGACCATAGCAGCAGCAGTTCTAGTGGCACAGAGCCGGGCAGCGGCGAGACGTA
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 | 37.30% | 36.80% | 1.90% | 23.99% | NA |
All Indica | 2759 | 5.40% | 54.20% | 3.23% | 37.11% | NA |
All Japonica | 1512 | 90.70% | 8.90% | 0.00% | 0.33% | NA |
Aus | 269 | 35.70% | 31.20% | 0.00% | 33.09% | NA |
Indica I | 595 | 6.10% | 86.90% | 0.00% | 7.06% | NA |
Indica II | 465 | 3.20% | 49.50% | 1.72% | 45.59% | NA |
Indica III | 913 | 2.70% | 40.10% | 6.68% | 50.49% | NA |
Indica Intermediate | 786 | 9.40% | 48.70% | 2.54% | 39.31% | NA |
Temperate Japonica | 767 | 98.40% | 1.00% | 0.00% | 0.52% | NA |
Tropical Japonica | 504 | 79.40% | 20.60% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 90.00% | 9.50% | 0.00% | 0.41% | NA |
VI/Aromatic | 96 | 83.30% | 8.30% | 0.00% | 8.33% | NA |
Intermediate | 90 | 71.10% | 18.90% | 1.11% | 8.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1218153472 | T -> C | LOC_Os12g30260.1 | missense_variant ; p.Thr290Ala; MODERATE | nonsynonymous_codon ; T290V | Average:52.193; most accessible tissue: Minghui63 young leaf, score: 69.4 | benign ![]() |
-0.118 ![]() |
TOLERATED | 0.05 |
vg1218153472 | T -> C | LOC_Os12g30260.1 | missense_variant ; p.Thr290Ala; MODERATE | nonsynonymous_codon ; T290A | Average:52.193; most accessible tissue: Minghui63 young leaf, score: 69.4 | possibly damaging ![]() |
-1.571 ![]() |
TOLERATED | 1.00 |
vg1218153472 | T -> DEL | LOC_Os12g30260.1 | N | frameshift_variant | Average:52.193; most accessible tissue: Minghui63 young leaf, score: 69.4 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1218153472 | 3.62E-06 | 2.64E-07 | mr1170 | 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 |
vg1218153472 | NA | 1.59E-06 | mr1864 | 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 |