| Variant ID: vg0432630329 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 32630329 |
| Reference Allele: TG | Alternative Allele: CG,T,TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG,TGCTCAAAACCCTATCGCTATCG |
| Primary Allele: TG | Secondary Allele: CG |
Inferred Ancestral Allele : TG (evidence from allele frequency in Oryza rufipogon: TG: 1.00, others allele: 0.00, population size: 88. )
TGCTAGCCAATTGGTTTTTAATGGATTATATTATTGTTATATTTTATTATCATCAACCGATTGTCTTTATATCATTATTTACATTGGAAATATAGCCGAT[TG/CG,T,TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG,TGCTCAAAACCCTATCGCTATCG]
GCTTTTCAGCCGATCGACTCATTGATCTACTATTTGCATATATTGTCAGTTACAGGGTCAAACTGACCGGCGCACCCGCATCTCATCAACCTTTGATCCT
AGGATCAAAGGTTGATGAGATGCGGGTGCGCCGGTCAGTTTGACCCTGTAACTGACAATATATGCAAATAGTAGATCAATGAGTCGATCGGCTGAAAAGC[CA/CG,A,CGATGGATTAATTCCAGCCGATATCTATACCAGCCGATAGCGATAGGGTTTTGAGCA,CGATAGCGATAGGGTTTTGAGCA]
ATCGGCTATATTTCCAATGTAAATAATGATATAAAGACAATCGGTTGATGATAATAAAATATAACAATAATATAATCCATTAAAAACCAATTGGCTAGCA
| Populations | Population Size | Frequency of TG(primary allele) | Frequency of CG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.70% | 0.90% | 9.01% | 3.07% | TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 0.70%; T: 0.53%; TGCTCAAAACCCTATCGCTATCG: 0.06% |
| All Indica | 2759 | 83.80% | 1.10% | 11.09% | 2.75% | TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 0.83%; T: 0.40%; TGCTCAAAACCCTATCGCTATCG: 0.07% |
| All Japonica | 1512 | 96.40% | 0.40% | 1.79% | 1.06% | TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 0.26%; T: 0.13% |
| Aus | 269 | 61.70% | 2.60% | 27.51% | 5.58% | TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 1.86%; T: 0.74% |
| Indica I | 595 | 91.80% | 0.50% | 6.89% | 0.34% | TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 0.50% |
| Indica II | 465 | 75.70% | 1.30% | 16.77% | 3.23% | TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 2.37%; T: 0.65% |
| Indica III | 913 | 83.00% | 1.90% | 9.09% | 4.82% | TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 0.66%; T: 0.44%; TGCTCAAAACCCTATCGCTATCG: 0.11% |
| Indica Intermediate | 786 | 83.30% | 0.50% | 13.23% | 1.91% | T: 0.51%; TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 0.38%; TGCTCAAAACCCTATCGCTATCG: 0.13% |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.13% | T: 0.13% |
| Tropical Japonica | 504 | 90.30% | 1.20% | 4.76% | 2.98% | TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 0.79% |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.83% | 0.00% | T: 0.41% |
| VI/Aromatic | 96 | 44.80% | 0.00% | 12.50% | 34.38% | T: 8.33% |
| Intermediate | 90 | 82.20% | 0.00% | 7.78% | 5.56% | T: 2.22%; TGCTCAAAACCCTATCGCTATCG: 1.11%; TGCTCAAAACCCTATCGCTATCGGCTGGTATAGATATCGGCTGGAATTAATCCATCG: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0432630329 | TG -> CG | LOC_Os04g54860.1 | upstream_gene_variant ; 1948.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> CG | LOC_Os04g54850.1 | downstream_gene_variant ; 1195.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> CG | LOC_Os04g54870.1 | downstream_gene_variant ; 2834.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> CG | LOC_Os04g54870.2 | downstream_gene_variant ; 2834.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> CG | LOC_Os04g54850-LOC_Os04g54860 | intergenic_region ; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCGGCTGGTA TAGATATCGGCTGGAATTAATCCATCG | LOC_Os04g54860.1 | upstream_gene_variant ; 1946.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCGGCTGGTA TAGATATCGGCTGGAATTAATCCATCG | LOC_Os04g54850.1 | downstream_gene_variant ; 1197.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCGGCTGGTA TAGATATCGGCTGGAATTAATCCATCG | LOC_Os04g54870.1 | downstream_gene_variant ; 2832.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCGGCTGGTA TAGATATCGGCTGGAATTAATCCATCG | LOC_Os04g54870.2 | downstream_gene_variant ; 2832.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCGGCTGGTA TAGATATCGGCTGGAATTAATCCATCG | LOC_Os04g54850-LOC_Os04g54860 | intergenic_region ; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> DEL | N | N | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCG | LOC_Os04g54860.1 | upstream_gene_variant ; 1946.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCG | LOC_Os04g54850.1 | downstream_gene_variant ; 1197.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCG | LOC_Os04g54870.1 | downstream_gene_variant ; 2832.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCG | LOC_Os04g54870.2 | downstream_gene_variant ; 2832.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> TGCTCAAAACCCTATCGCTATCG | LOC_Os04g54850-LOC_Os04g54860 | intergenic_region ; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> T | LOC_Os04g54860.1 | upstream_gene_variant ; 1947.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> T | LOC_Os04g54850.1 | downstream_gene_variant ; 1196.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> T | LOC_Os04g54870.1 | downstream_gene_variant ; 2833.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> T | LOC_Os04g54870.2 | downstream_gene_variant ; 2833.0bp to feature; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| vg0432630329 | TG -> T | LOC_Os04g54850-LOC_Os04g54860 | intergenic_region ; MODIFIER | silent_mutation | Average:35.024; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0432630329 | 4.61E-07 | 1.85E-08 | mr1076 | 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 |
| vg0432630329 | NA | 2.11E-07 | mr1082 | 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 |
| vg0432630329 | 1.69E-06 | 3.79E-09 | mr1083 | 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 |
| vg0432630329 | 7.73E-06 | NA | mr1104 | 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 |
| vg0432630329 | 3.61E-06 | 3.61E-06 | mr1204 | 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 |
| vg0432630329 | 1.48E-07 | 2.60E-09 | mr1226 | 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 |
| vg0432630329 | NA | 6.01E-06 | mr1227 | 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 |
| vg0432630329 | NA | 5.66E-06 | mr1233 | 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 |
| vg0432630329 | NA | 2.07E-06 | mr1304 | 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 |
| vg0432630329 | NA | 2.49E-06 | mr1364 | 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 |
| vg0432630329 | NA | 6.32E-06 | mr1382 | 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 |
| vg0432630329 | 5.73E-06 | 4.99E-07 | mr1408 | 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 |
| vg0432630329 | 3.93E-08 | 6.98E-07 | mr1411 | 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 |
| vg0432630329 | NA | 1.73E-06 | mr1443 | 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 |
| vg0432630329 | 3.87E-06 | 2.38E-07 | mr1560 | 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 |
| vg0432630329 | 4.71E-06 | 3.44E-06 | mr1878 | 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 |
| vg0432630329 | 8.25E-06 | 1.10E-06 | mr1949 | 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 |
| vg0432630329 | NA | 4.20E-06 | mr1194_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 |
| vg0432630329 | NA | 1.47E-06 | mr1226_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 |
| vg0432630329 | 7.63E-07 | 3.78E-09 | mr1243_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 |
| vg0432630329 | NA | 1.81E-07 | mr1423_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 |
| vg0432630329 | 9.66E-06 | 7.33E-08 | mr1498_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 |
| vg0432630329 | 4.27E-07 | NA | mr1800_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 |
| vg0432630329 | 6.59E-10 | 4.89E-14 | mr1800_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 |