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Detailed information for vg0319757135:
| Variant ID: vg0319757135 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 19757135 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
GTTGTTGGTGGTATCATCATCATTAGTATTGCTAGTGTTGTTGTCTGCATTGCGTCCATCTTCTTGGGGCAGGAACTCTTGATGCACAACAGAAGATCCG[G/A]
TGATCTGAAGTGGCTCAGTGCGCTGTCTTTGGTTACCACATGGAAATACTGGGATGTTGACAATCCTCCTCTTGCAGTTCGTCATCCGATTATGCTCACT
Reverse complement sequence
AGTGAGCATAATCGGATGACGAACTGCAAGAGGAGGATTGTCAACATCCCAGTATTTCCATGTGGTAACCAAAGACAGCGCACTGAGCCACTTCAGATCA[C/T]
CGGATCTTCTGTTGTGCATCAAGAGTTCCTGCCCCAAGAAGATGGACGCAATGCAGACAACAACACTAGCAATACTAATGATGATGATACCACCAACAAC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.10% | 0.30% | 3.32% | 61.36% | NA |
| All Indica | 2759 | 8.60% | 0.30% | 4.24% | 86.88% | NA |
| All Japonica | 1512 | 83.80% | 0.00% | 1.98% | 14.22% | NA |
| Aus | 269 | 12.60% | 0.40% | 0.37% | 86.62% | NA |
| Indica I | 595 | 4.90% | 0.20% | 1.34% | 93.61% | NA |
| Indica II | 465 | 8.00% | 0.00% | 3.01% | 89.03% | NA |
| Indica III | 913 | 10.80% | 0.40% | 6.90% | 81.82% | NA |
| Indica Intermediate | 786 | 9.00% | 0.50% | 4.07% | 86.39% | NA |
| Temperate Japonica | 767 | 94.40% | 0.00% | 0.13% | 5.48% | NA |
| Tropical Japonica | 504 | 66.50% | 0.00% | 4.96% | 28.57% | NA |
| Japonica Intermediate | 241 | 86.30% | 0.00% | 1.66% | 12.03% | NA |
| VI/Aromatic | 96 | 74.00% | 2.10% | 3.12% | 20.83% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 6.67% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757135 | G -> A | LOC_Os03g35670.1 | missense_variant ; p.Thr630Ile; MODERATE | nonsynonymous_codon ; T630I | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.472 |
TOLERATED | 0.08 |
| vg0319757135 | G -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |