| Variant ID: vg1004719297 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4719297 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.24, others allele: 0.00, population size: 86. )
CAAGTAATCAAGCACTCTCTTTGCAACGTAGCCCCTCTATCAGAATAGAAATTCAAGAAGTACCATTTCTGGCCAATCTTACCCTGTTAGAATCCAAAGA[T/C]
CTTGATGTCATCCTAGGGATGGACTGGTTAGCCAGATATAAAGGTGTGATAGACTGTGCCAACAGAAAAGTAACTCTCACCAGCAATGATGGTCGAGTTG
CAACTCGACCATCATTGCTGGTGAGAGTTACTTTTCTGTTGGCACAGTCTATCACACCTTTATATCTGGCTAACCAGTCCATCCCTAGGATGACATCAAG[A/G]
TCTTTGGATTCTAACAGGGTAAGATTGGCCAGAAATGGTACTTCTTGAATTTCTATTCTGATAGAGGGGCTACGTTGCAAAGAGAGTGCTTGATTACTTG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 17.00% | 1.20% | 29.71% | 52.03% | NA |
| All Indica | 2759 | 2.60% | 1.60% | 23.38% | 72.35% | NA |
| All Japonica | 1512 | 45.70% | 0.90% | 41.47% | 11.90% | NA |
| Aus | 269 | 2.20% | 0.00% | 7.43% | 90.33% | NA |
| Indica I | 595 | 1.70% | 0.70% | 19.83% | 77.82% | NA |
| Indica II | 465 | 3.00% | 1.90% | 23.23% | 71.83% | NA |
| Indica III | 913 | 2.30% | 2.10% | 27.93% | 67.69% | NA |
| Indica Intermediate | 786 | 3.60% | 1.70% | 20.87% | 73.92% | NA |
| Temperate Japonica | 767 | 81.50% | 0.50% | 11.08% | 6.91% | NA |
| Tropical Japonica | 504 | 3.60% | 1.80% | 82.34% | 12.30% | NA |
| Japonica Intermediate | 241 | 19.90% | 0.40% | 52.70% | 26.97% | NA |
| VI/Aromatic | 96 | 17.70% | 0.00% | 75.00% | 7.29% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 44.44% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004719297 | T -> C | LOC_Os10g08702.1 | synonymous_variant ; p.Asp395Asp; LOW | synonymous_codon | Average:12.224; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1004719297 | T -> DEL | LOC_Os10g08702.1 | N | frameshift_variant | Average:12.224; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004719297 | NA | 2.70E-08 | mr1248 | 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 |
| vg1004719297 | NA | 5.12E-07 | mr1310 | 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 |
| vg1004719297 | NA | 1.49E-06 | mr1471 | 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 |
| vg1004719297 | NA | 2.18E-06 | mr1742 | 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 |
| vg1004719297 | NA | 9.61E-07 | mr1870 | 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 |
| vg1004719297 | NA | 3.80E-08 | mr1310_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 |
| vg1004719297 | NA | 4.05E-12 | mr1533_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 |
| vg1004719297 | 9.08E-06 | NA | mr1622_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 |
| vg1004719297 | NA | 5.91E-06 | mr1959_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 |