| Variant ID: vg1001363789 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 1363789 |
| Reference Allele: CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA | Alternative Allele: C,TGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA,CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA |
| Primary Allele: CGATAAGCATTAAAAAGAAG TACATACTTACAAGATGAGA CATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA | Secondary Allele: TGATAAGCATTAAAAAGAAG TACATACTTACAAGATGAGA CATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA |
Inferred Ancestral Allele: Not determined.
TGTGCTTTTAAGCCTAGTTATGTTTATGATATCTTTTTTAGATCTCGGAAAGGGTTCTTCATAAAATTGATTATTATAGATCATGTTTCTTTTGACAAGG[CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA/C,TGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA,CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA]
GTTCACAACTTAGAAATTCAAAACCAGTATATGTTGAGTAAATTGTTATTTAAGTTAATTAATGAGCAGGGGGTTTGGCAAGATTTATTGAAAAGGAAAT
ATTTCCTTTTCAATAAATCTTGCCAAACCCCCTGCTCATTAATTAACTTAAATAACAATTTACTCAACATATACTGGTTTTGAATTTCTAAGTTGTGAAC[TCCAAGACCACCCTGCTCTTTGGGCTGACATATAATGTCTCATCTTGTAAGTATGTACTTCTTTTTAATGCTTATCG/G,TCCAAGACCACCCTGCTCTTTGGGCTGACATATAATGTCTCATCTTGTAAGTATGTACTTCTTTTTAATGCTTATCA,TCCAAGACCACCCTGCTCTTTGGGCTGACATATAATGTCTCATCTTGTAAGTATGTACTTCTTTTTAATGCTTATCCCCTCAAAAAAAAATTCTAAGTTGTGAACG]
CCTTGTCAAAAGAAACATGATCTATAATAATCAATTTTATGAAGAACCCTTTCCGAGATCTAAAAAAGATATCATAAACATAACTAGGCTTAAAAGCACA
| Populations | Population Size | Frequency of CGATAAGCATTAAAAAGAAG TACATACTTACAAGATGAGA CATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA(primary allele) | Frequency of TGATAAGCATTAAAAAGAAG TACATACTTACAAGATGAGA CATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.40% | 7.80% | 1.16% | 0.00% | C: 6.60%; CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA: 0.06% |
| All Indica | 2759 | 73.70% | 13.00% | 1.92% | 0.00% | C: 11.24%; CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA: 0.11% |
| All Japonica | 1512 | 99.70% | 0.10% | 0.07% | 0.00% | C: 0.07% |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 73.30% | 1.30% | 2.86% | 0.00% | C: 22.35%; CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA: 0.17% |
| Indica II | 465 | 59.60% | 29.20% | 2.58% | 0.00% | C: 8.17%; CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA: 0.43% |
| Indica III | 913 | 75.70% | 14.20% | 0.77% | 0.00% | C: 9.31% |
| Indica Intermediate | 786 | 80.20% | 10.80% | 2.16% | 0.00% | C: 6.87% |
| Temperate Japonica | 767 | 99.70% | 0.10% | 0.00% | 0.00% | C: 0.13% |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 6.70% | 1.11% | 0.00% | C: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> TGATAAGCATTAAAAAGAAGTACATACTTA CAAGATGAGACATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA | LOC_Os10g03240.1 | upstream_gene_variant ; 2827.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> TGATAAGCATTAAAAAGAAGTACATACTTA CAAGATGAGACATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA | LOC_Os10g03220.1 | downstream_gene_variant ; 4608.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> TGATAAGCATTAAAAAGAAGTACATACTTA CAAGATGAGACATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA | LOC_Os10g03230.1 | downstream_gene_variant ; 3473.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> TGATAAGCATTAAAAAGAAGTACATACTTA CAAGATGAGACATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA | LOC_Os10g03230-LOC_Os10g03240 | intergenic_region ; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> C | LOC_Os10g03240.1 | upstream_gene_variant ; 2826.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> C | LOC_Os10g03220.1 | downstream_gene_variant ; 4609.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> C | LOC_Os10g03230.1 | downstream_gene_variant ; 3474.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> C | LOC_Os10g03230-LOC_Os10g03240 | intergenic_region ; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> CGTTCACAACTTAGAATTTTTTTTTGAGGG GATAAGCATTAAAAAGAAGTACATACTTAC AAGATGAGACATTATATGTCAGCCCAAAGA GCAGGGTGGTCTTGGA | LOC_Os10g03240.1 | upstream_gene_variant ; 2825.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> CGTTCACAACTTAGAATTTTTTTTTGAGGG GATAAGCATTAAAAAGAAGTACATACTTAC AAGATGAGACATTATATGTCAGCCCAAAGA GCAGGGTGGTCTTGGA | LOC_Os10g03220.1 | downstream_gene_variant ; 4610.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> CGTTCACAACTTAGAATTTTTTTTTGAGGG GATAAGCATTAAAAAGAAGTACATACTTAC AAGATGAGACATTATATGTCAGCCCAAAGA GCAGGGTGGTCTTGGA | LOC_Os10g03230.1 | downstream_gene_variant ; 3475.0bp to feature; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| vg1001363789 | CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> CGTTCACAACTTAGAATTTTTTTTTGAGGG GATAAGCATTAAAAAGAAGTACATACTTAC AAGATGAGACATTATATGTCAGCCCAAAGA GCAGGGTGGTCTTGGA | LOC_Os10g03230-LOC_Os10g03240 | intergenic_region ; MODIFIER | silent_mutation | Average:33.503; most accessible tissue: Callus, score: 53.84 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1001363789 | 9.74E-16 | NA | mr1486 | 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 |
| vg1001363789 | 2.32E-18 | 2.53E-15 | mr1486 | 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 |
| vg1001363789 | 1.90E-14 | NA | mr1548 | 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 |
| vg1001363789 | 2.29E-14 | 3.01E-11 | mr1548 | 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 |
| vg1001363789 | 6.23E-10 | NA | mr1588 | 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 |
| vg1001363789 | 9.55E-12 | 9.47E-12 | mr1588 | 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 |
| vg1001363789 | NA | 8.56E-08 | mr1158_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 |
| vg1001363789 | NA | 2.68E-08 | mr1158_2 | 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 |
| vg1001363789 | 2.12E-16 | NA | mr1486_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 |
| vg1001363789 | 1.12E-19 | 5.31E-20 | mr1486_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 |
| vg1001363789 | 4.81E-14 | NA | mr1588_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 |
| vg1001363789 | 1.24E-15 | 2.05E-16 | mr1588_2 | 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 |