| Variant ID: vg0723622803 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 23622803 |
| Reference Allele: T | Alternative Allele: G,TG |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 286. )
GCCTGGGTTGCTGTGCTGGTATTCAATCATCAGCATTCGGCACACATATATCAATATCACAGATACATCACTAACTACAGTTTAGACTTCCTTTTTTTTT[T/G,TG]
ACTCCTATTACAACAAGGTGTAAATTCTTCATCTGATTCCTCCAGTCGAAAAACAAATGGATGTTCCAGGAGTCAATCTAAGGATGAAAAGGGATGCACC
GGTGCATCCCTTTTCATCCTTAGATTGACTCCTGGAACATCCATTTGTTTTTCGACTGGAGGAATCAGATGAAGAATTTACACCTTGTTGTAATAGGAGT[A/C,CA]
AAAAAAAAAGGAAGTCTAAACTGTAGTTAGTGATGTATCTGTGATATTGATATATGTGTGCCGAATGCTGATGATTGAATACCAGCACAGCAACCCAGGC
| 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 | 87.60% | 12.30% | 0.06% | 0.00% | TG: 0.04% |
| All Indica | 2759 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 80.00% | 19.90% | 0.07% | 0.00% | NA |
| Aus | 269 | 43.50% | 56.10% | 0.00% | 0.00% | TG: 0.37% |
| Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.80% | 9.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 70.80% | 29.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 65.60% | 34.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 72.90% | 24.00% | 2.08% | 0.00% | TG: 1.04% |
| Intermediate | 90 | 88.90% | 11.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0723622803 | T -> G | LOC_Os07g39430.1 | 3_prime_UTR_variant ; 249.0bp to feature; MODIFIER | silent_mutation | Average:60.443; most accessible tissue: Callus, score: 90.958 | N | N | N | N |
| vg0723622803 | T -> G | LOC_Os07g39440.1 | downstream_gene_variant ; 1561.0bp to feature; MODIFIER | silent_mutation | Average:60.443; most accessible tissue: Callus, score: 90.958 | N | N | N | N |
| vg0723622803 | T -> TG | LOC_Os07g39430.1 | 3_prime_UTR_variant ; 250.0bp to feature; MODIFIER | silent_mutation | Average:60.443; most accessible tissue: Callus, score: 90.958 | N | N | N | N |
| vg0723622803 | T -> TG | LOC_Os07g39440.1 | downstream_gene_variant ; 1560.0bp to feature; MODIFIER | silent_mutation | Average:60.443; most accessible tissue: Callus, score: 90.958 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0723622803 | NA | 8.68E-06 | mr1594_2 | Jap_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 |
| vg0723622803 | 4.16E-06 | NA | mr1865_2 | 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 |
| vg0723622803 | NA | 5.69E-09 | mr1865_2 | Jap_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 |