Search for Variation information by Variation ID:
Detailed information for vg0715978134:
| Variant ID: vg0715978134 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 15978134 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 204. )
Flanking Sequence (100 bp) in Reference Genome:
TAAAGTTTTTAGACAGCAGATTCAGGTGGCTATTGAAGGGGGCAAGATTAAGTTCGATGACTCCAAGAAGCCGATGAAGGTCGATGGCAATCCTTTTCCT[A/G]
TTAATATGGTGCATACAGCTAGCCAGACAGTCGACAGGATCCGTGCAAAGGGTTTTCAGGTGAATTCGGCTAGGGTTATCAACAAATATCAGAGGAAATA
Reverse complement sequence
TATTTCCTCTGATATTTGTTGATAACCCTAGCCGAATTCACCTGAAAACCCTTTGCACGGATCCTGTCGACTGTCTGGCTAGCTGTATGCACCATATTAA[T/C]
AGGAAAAGGATTGCCATCGACCTTCATCGGCTTCTTGGAGTCATCGAACTTAATCTTGCCCCCTTCAATAGCCACCTGAATCTGCTGTCTAAAAACTTTA
Allele Frequencies:
| 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 | 39.20% | 36.50% | 2.94% | 21.35% | NA |
| All Indica | 2759 | 10.80% | 48.70% | 4.86% | 35.63% | NA |
| All Japonica | 1512 | 92.80% | 6.50% | 0.07% | 0.66% | NA |
| Aus | 269 | 6.30% | 93.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 22.50% | 47.70% | 4.71% | 25.04% | NA |
| Indica II | 465 | 8.00% | 17.20% | 3.87% | 70.97% | NA |
| Indica III | 913 | 3.50% | 61.00% | 4.60% | 30.89% | NA |
| Indica Intermediate | 786 | 12.10% | 53.80% | 5.85% | 28.24% | NA |
| Temperate Japonica | 767 | 87.70% | 11.30% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 98.00% | 1.60% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.20% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 26.70% | 4.44% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0715978134 | A -> DEL | LOC_Os07g27420.1 | N | frameshift_variant | Average:14.092; most accessible tissue: Zhenshan97 flag leaf, score: 25.809 | N | N | N | N |
| vg0715978134 | A -> G | LOC_Os07g27420.1 | missense_variant ; p.Ile771Val; MODERATE | nonsynonymous_codon ; I771V | Average:14.092; most accessible tissue: Zhenshan97 flag leaf, score: 25.809 | benign  |
-0.555 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0715978134 | NA | 4.24E-09 | mr1005 | 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 |
| vg0715978134 | 6.64E-08 | 2.71E-07 | mr1018 | 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 |
| vg0715978134 | NA | 2.74E-10 | mr1630 | 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 |
| vg0715978134 | NA | 3.90E-07 | mr1915 | 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 |
| vg0715978134 | 4.86E-06 | 4.86E-06 | mr1528_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 |