| Variant ID: vg1002030590 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 2030590 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 78. )
CATTCACACAAGACGGTTTACATGGGTCGCAGGAGATTTCTCCCAAGGTATCACCCATATAGGAATATGAAAAAGAATTTCAAGGGACACAGAGATACAG[T/C]
CGGACCCCCGGCAGAGCTAACAGGGACTGAGGTGCACAACTTAGTGATGGGAATAACAAACAAGTTTGGAAAAAAGAGGAAAGTTGGAAAGACAAAAGAG
CTCTTTTGTCTTTCCAACTTTCCTCTTTTTTCCAAACTTGTTTGTTATTCCCATCACTAAGTTGTGCACCTCAGTCCCTGTTAGCTCTGCCGGGGGTCCG[A/G]
CTGTATCTCTGTGTCCCTTGAAATTCTTTTTCATATTCCTATATGGGTGATACCTTGGGAGAAATCTCCTGCGACCCATGTAAACCGTCTTGTGTGAATG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.70% | 33.80% | 3.85% | 5.59% | NA |
| All Indica | 2759 | 59.60% | 34.50% | 4.82% | 1.09% | NA |
| All Japonica | 1512 | 58.90% | 35.60% | 0.79% | 4.70% | NA |
| Aus | 269 | 4.50% | 26.00% | 13.01% | 56.51% | NA |
| Indica I | 595 | 52.10% | 44.00% | 3.87% | 0.00% | NA |
| Indica II | 465 | 70.30% | 24.90% | 4.52% | 0.22% | NA |
| Indica III | 913 | 55.20% | 36.90% | 6.90% | 0.99% | NA |
| Indica Intermediate | 786 | 64.00% | 30.20% | 3.31% | 2.54% | NA |
| Temperate Japonica | 767 | 50.70% | 48.40% | 0.26% | 0.65% | NA |
| Tropical Japonica | 504 | 81.20% | 6.50% | 1.19% | 11.11% | NA |
| Japonica Intermediate | 241 | 38.20% | 56.00% | 1.66% | 4.15% | NA |
| VI/Aromatic | 96 | 85.40% | 9.40% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 58.90% | 32.20% | 2.22% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1002030590 | T -> C | LOC_Os10g04290.1 | missense_variant ; p.Val1727Ala; MODERATE | nonsynonymous_codon ; V1727A | Average:20.27; most accessible tissue: Minghui63 young leaf, score: 31.294 | unknown | unknown | TOLERATED | 0.84 |
| vg1002030590 | T -> DEL | LOC_Os10g04290.1 | N | frameshift_variant | Average:20.27; most accessible tissue: Minghui63 young leaf, score: 31.294 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1002030590 | 8.15E-07 | 3.74E-07 | mr1638_2 | 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 |
| vg1002030590 | 2.62E-06 | 2.87E-06 | mr1741_2 | 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 |