15 variations found. LOC_Os04g33420 (DNA-binding protein S1FA; putative; expressed), ranging from 20,229,221 bp to 20,230,813 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| STR0420229431 (J) | chr04 | 20229431 | TGTTG | TGTTA | 95.30% | 0.00% | TGTTG -> TGTTA | NA |
|
| vg0420229435 (J) | chr04 | 20229435 | G | A | 95.00% | 0.00% | G -> A | NA |
LOC_Os04g33420.1 Alt: A| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.540; most accessible tissue: Zhenshan97 flower, score: 87.488 |
| vg0420229492 (J) | chr04 | 20229492 | T | A | 86.50% | 0.00% | T -> A | NA |
LOC_Os04g33440.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.823; most accessible tissue: Zhenshan97 flower, score: 87.106 |
| vg0420229545 (J) | chr04 | 20229545 | A | C | 99.10% | 0.00% | A -> C | NA |
LOC_Os04g33440.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33430.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.488; most accessible tissue: Zhenshan97 flower, score: 85.053 |
| vg0420229661 (J) | chr04 | 20229661 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os04g33440.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.363; most accessible tissue: Zhenshan97 flower, score: 81.460 |
| vg0420229772 (J) | chr04 | 20229772 | C | G | 99.30% | 0.00% | C -> G | NA |
LOC_Os04g33440.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33430.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.488; most accessible tissue: Callus, score: 86.283 |
| vg0420229925 (J) | chr04 | 20229925 | A | C | 59.60% | 0.55% | C -> A |
mr1100 (All); LR P-value: 1.77E-76;
mr1619 (All); LR P-value: 1.98E-67; mr1723 (All); LR P-value: 9.69E-28; mr1795 (All); LR P-value: 5.80E-55; mr1861 (All); LR P-value: 1.23E-53; mr1865 (All); LR P-value: 1.23E-68; mr1962 (All); LR P-value: 3.03E-60; mr1035_2 (All); LR P-value: 4.89E-13; mr1040_2 (All); LR P-value: 7.02E-16; mr1100_2 (All); LR P-value: 9.18E-100; mr1216_2 (All); LR P-value: 6.67E-11; mr1281_2 (All); LR P-value: 7.32E-18; mr1299_2 (All); LR P-value: 2.57E-08; mr1362_2 (All); LR P-value: 2.39E-20; mr1537_2 (All); LR P-value: 4.13E-12; mr1541_2 (All); LR P-value: 1.18E-37; mr1592_2 (All); LR P-value: 5.12E-17; mr1609_2 (All); LR P-value: 7.70E-24; mr1619_2 (All); LR P-value: 8.35E-102; mr1631_2 (All); LR P-value: 1.10E-30; mr1712_2 (All); LR P-value: 7.54E-18; mr1713_2 (All); LR P-value: 2.50E-12; mr1727_2 (All); LR P-value: 7.06E-07; mr1770_2 (All); LR P-value: 5.71E-14; mr1783_2 (All); LR P-value: 2.11E-08; mr1795_2 (All); LR P-value: 4.37E-90; mr1804_2 (All); LR P-value: 8.60E-08; mr1841_2 (All); LR P-value: 4.13E-32; mr1861_2 (All); LR P-value: 2.01E-47; mr1888_2 (All); LR P-value: 3.63E-35 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33440.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.562; most accessible tissue: Callus, score: 85.692 |
| vg0420230101 (J) | chr04 | 20230101 | A | G | 61.90% | 0.13% | G -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33440.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.102; most accessible tissue: Minghui63 flower, score: 82.376 |
|
| vg0420230253 (J) | chr04 | 20230253 | A | C | 59.60% | 0.55% | C -> A |
mr1100 (All); LR P-value: 8.30E-77;
mr1619 (All); LR P-value: 1.58E-67; mr1723 (All); LR P-value: 1.01E-27; mr1795 (All); LR P-value: 3.09E-55; mr1861 (All); LR P-value: 6.51E-54; mr1865 (All); LR P-value: 8.06E-69; mr1962 (All); LR P-value: 2.89E-60; mr1035_2 (All); LR P-value: 5.39E-13; mr1040_2 (All); LR P-value: 7.91E-16; mr1100_2 (All); LR P-value: 4.53E-100; mr1281_2 (All); LR P-value: 7.69E-18; mr1299_2 (All); LR P-value: 2.91E-08; mr1362_2 (All); LR P-value: 2.85E-20; mr1537_2 (All); LR P-value: 5.39E-12; mr1541_2 (All); LR P-value: 1.48E-37; mr1592_2 (All); LR P-value: 6.51E-17; mr1609_2 (All); LR P-value: 6.07E-24; mr1619_2 (All); LR P-value: 7.45E-102; mr1631_2 (All); LR P-value: 1.03E-30; mr1712_2 (All); LR P-value: 6.16E-18; mr1727_2 (All); LR P-value: 8.14E-07; mr1770_2 (All); LR P-value: 6.63E-14; mr1783_2 (All); LR P-value: 2.59E-08; mr1795_2 (All); LR P-value: 2.72E-90; mr1804_2 (All); LR P-value: 9.70E-08; mr1841_2 (All); LR P-value: 3.01E-32; mr1861_2 (All); LR P-value: 1.43E-47; mr1888_2 (All); LR P-value: 3.63E-35 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33440.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.755; most accessible tissue: Minghui63 flower, score: 86.453 |
| vg0420230376 (J) | chr04 | 20230376 | C | T | 96.10% | 0.00% | C -> T | NA |
LOC_Os04g33440.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33430.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.762; most accessible tissue: Minghui63 flower, score: 90.393 |
| vg0420230428 (J) | chr04 | 20230428 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os04g33440.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33430.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.790; most accessible tissue: Minghui63 flower, score: 91.725 |
| vg0420230499 (J) | chr04 | 20230499 | C | G | 99.10% | 0.00% | C -> G | NA |
LOC_Os04g33440.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33430.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.370; most accessible tissue: Minghui63 flower, score: 93.236 |
| vg0420230507 (J) | chr04 | 20230507 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os04g33440.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33430.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.854; most accessible tissue: Minghui63 flower, score: 93.290 |
| vg0420230575 (J) | chr04 | 20230575 | T | TG | 99.90% | 0.00% | T -> TG | NA |
LOC_Os04g33440.2 Alt: TG| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33430.1 Alt: TG| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33410.1 Alt: TG| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: TG| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.478; most accessible tissue: Minghui63 flower, score: 95.716 |
| vg0420230592 (J) | chr04 | 20230592 | T | C | 60.10% | 0.57% | C -> T |
mr1723 (All); LR P-value: 2.23E-27;
mr1795 (All); LR P-value: 9.07E-54; mr1861 (All); LR P-value: 5.80E-54; mr1035_2 (All); LR P-value: 3.35E-13; mr1040_2 (All); LR P-value: 6.43E-16; mr1072_2 (All); LR P-value: 1.41E-37; mr1238_2 (All); LR P-value: 1.02E-27; mr1281_2 (All); LR P-value: 4.05E-18; mr1299_2 (All); LR P-value: 3.25E-08; mr1362_2 (All); LR P-value: 2.74E-20; mr1416_2 (All); LR P-value: 4.77E-16; mr1537_2 (All); LR P-value: 2.12E-12; mr1541_2 (All); LR P-value: 1.34E-37; mr1592_2 (All); LR P-value: 5.80E-17; mr1609_2 (All); LR P-value: 2.24E-24; mr1631_2 (All); LR P-value: 5.21E-31; mr1708_2 (All); LR P-value: 3.77E-23; mr1712_2 (All); LR P-value: 7.10E-18; mr1713_2 (All); LR P-value: 2.74E-12; mr1717_2 (All); LR P-value: 9.89E-13; mr1727_2 (All); LR P-value: 5.27E-07; mr1770_2 (All); LR P-value: 2.58E-14; mr1783_2 (All); LR P-value: 1.51E-08; mr1795_2 (All); LR P-value: 2.92E-88; mr1804_2 (All); LR P-value: 4.85E-08; mr1841_2 (All); LR P-value: 6.58E-33; mr1861_2 (All); LR P-value: 1.27E-48; mr1900_2 (All); LR P-value: 7.58E-20; mr1916_2 (All); LR P-value: 3.52E-24 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33440.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33410.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.292; most accessible tissue: Minghui63 flower, score: 95.759 |
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