| Variant ID: vg1206195784 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 6195784 |
| Reference Allele: G | Alternative Allele: A,GAAA,GAAATTCAT,GAAATTCA |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 69. )
CGCTTCGTGGTTTTGGCGGTAGAGAAGTTCAAGTTTTGGGCCAAGTACAACTGGTGGTAGCTTTCGGCACAAGTGAAAACAGGCGCGTAGAGCAAATACT[G/A,GAAA,GAAATTCAT,GAAATTCA]
TTCGATGTCGTCGACATCCCATACAACTACAATGCCATCTTCGGCCGCGCAATCTTGAACAAGTTCGAAGCCATCTCCCACCACAACTACCTCAAGCTCA
TGAGCTTGAGGTAGTTGTGGTGGGAGATGGCTTCGAACTTGTTCAAGATTGCGCGGCCGAAGATGGCATTGTAGTTGTATGGGATGTCGACGACATCGAA[C/T,TTTC,ATGAATTTC,TGAATTTC]
AGTATTTGCTCTACGCGCCTGTTTTCACTTGTGCCGAAAGCTACCACCAGTTGTACTTGGCCCAAAACTTGAACTTCTCTACCGCCAAAACCACGAAGCG
| 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 | 46.70% | 35.10% | 8.57% | 9.16% | GAAA: 0.19%; GAAATTCAT: 0.11%; GAAATTCA: 0.08% |
| All Indica | 2759 | 66.20% | 16.10% | 13.48% | 3.59% | GAAA: 0.33%; GAAATTCAT: 0.18%; GAAATTCA: 0.11% |
| All Japonica | 1512 | 9.40% | 71.00% | 1.06% | 18.45% | GAAATTCA: 0.07% |
| Aus | 269 | 42.80% | 36.80% | 3.35% | 17.10% | NA |
| Indica I | 595 | 21.30% | 31.40% | 41.85% | 3.36% | GAAA: 1.34%; GAAATTCA: 0.34%; GAAATTCAT: 0.34% |
| Indica II | 465 | 77.20% | 9.00% | 3.44% | 10.32% | NA |
| Indica III | 913 | 91.90% | 6.50% | 0.88% | 0.66% | GAAA: 0.11% |
| Indica Intermediate | 786 | 63.90% | 19.80% | 12.60% | 3.18% | GAAATTCAT: 0.38%; GAAATTCA: 0.13% |
| Temperate Japonica | 767 | 14.50% | 58.50% | 1.30% | 25.55% | GAAATTCA: 0.13% |
| Tropical Japonica | 504 | 4.60% | 85.90% | 0.79% | 8.73% | NA |
| Japonica Intermediate | 241 | 3.30% | 79.70% | 0.83% | 16.18% | NA |
| VI/Aromatic | 96 | 89.60% | 4.20% | 6.25% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 44.40% | 2.22% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206195784 | G -> A | LOC_Os12g11450.1 | upstream_gene_variant ; 2202.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> A | LOC_Os12g11470.1 | upstream_gene_variant ; 1871.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> A | LOC_Os12g11460.1 | downstream_gene_variant ; 297.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> A | LOC_Os12g11460-LOC_Os12g11470 | intergenic_region ; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAATTCA | LOC_Os12g11450.1 | upstream_gene_variant ; 2203.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAATTCA | LOC_Os12g11470.1 | upstream_gene_variant ; 1870.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAATTCA | LOC_Os12g11460.1 | downstream_gene_variant ; 298.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAATTCA | LOC_Os12g11460-LOC_Os12g11470 | intergenic_region ; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAATTCAT | LOC_Os12g11450.1 | upstream_gene_variant ; 2203.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAATTCAT | LOC_Os12g11470.1 | upstream_gene_variant ; 1870.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAATTCAT | LOC_Os12g11460.1 | downstream_gene_variant ; 298.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAATTCAT | LOC_Os12g11460-LOC_Os12g11470 | intergenic_region ; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAA | LOC_Os12g11450.1 | upstream_gene_variant ; 2203.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAA | LOC_Os12g11470.1 | upstream_gene_variant ; 1870.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAA | LOC_Os12g11460.1 | downstream_gene_variant ; 298.0bp to feature; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> GAAA | LOC_Os12g11460-LOC_Os12g11470 | intergenic_region ; MODIFIER | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| vg1206195784 | G -> DEL | N | N | silent_mutation | Average:13.16; most accessible tissue: Callus, score: 32.711 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1206195784 | 5.08E-06 | 5.08E-06 | mr1024 | 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 |
| vg1206195784 | NA | 4.23E-07 | mr1531 | 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 |
| vg1206195784 | 7.07E-07 | 1.48E-06 | mr1940 | Jap_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 |
| vg1206195784 | NA | 8.14E-15 | mr1565_2 | 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 |
| vg1206195784 | 1.88E-06 | 9.22E-06 | mr1565_2 | Jap_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 |