26 variations found. LOC_Os04g33440 (DNA-binding protein S1FA; putative; expressed), ranging from 20,224,554 bp to 20,226,415 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0420224561 (J) | chr04 | 20224561 | T | C | 99.10% | 0.00% | T -> C | NA |
LOC_Os04g33440.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33450.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.805; most accessible tissue: Callus, score: 81.157 |
| vg0420224566 (J) | chr04 | 20224566 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os04g33440.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.805; most accessible tissue: Callus, score: 81.157 |
| vg0420224587 (J) | chr04 | 20224587 | C | G | 99.40% | 0.00% | C -> G | NA |
LOC_Os04g33440.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g33450.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.3 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 61.782; most accessible tissue: Zhenshan97 flower, score: 81.984 |
| vg0420224622 (J) | chr04 | 20224622 | G | GAC | 31.00% | 57.83% | G -> GAC | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33440.2 Alt: GAC| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.1 Alt: GAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: GAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: GAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: GAC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: GAC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 |
| vg0420224624 (J) | chr04 | 20224624 | CAG | C | 61.80% | 0.08% | C -> CAG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33440.2 Alt: CAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.1 Alt: CAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: CAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: CAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: CAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: CAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.739; most accessible tissue: Zhenshan97 flower, score: 82.834 |
| vg0420224655 (J) | chr04 | 20224655 | ATTGCAG | A | 61.90% | 0.55% | A -> ATTGCAG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33440.2 Alt: ATTGCAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.1 Alt: ATTGCAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: ATTGCAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: ATTGCAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: ATTGCAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: ATTGCAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.632; most accessible tissue: Zhenshan97 flower, score: 83.392 |
| vg0420224800 (J) | chr04 | 20224800 | T | C | 50.60% | 0.38% | C -> T |
mr1208 (All); LR P-value: 8.36E-30;
mr1299 (All); LR P-value: 6.34E-10; mr1321 (All); LR P-value: 7.78E-07; mr1551 (All); LR P-value: 1.93E-25; mr1552 (All); LR P-value: 1.39E-18; mr1598 (All); LR P-value: 1.09E-18; mr1648 (All); LR P-value: 8.51E-09; mr1655 (All); LR P-value: 6.14E-15; mr1700 (All); LR P-value: 2.70E-18; mr1713 (All); LR P-value: 8.55E-12; mr1717 (All); LR P-value: 4.12E-07; mr1756 (All); LR P-value: 6.06E-07; mr1770 (All); LR P-value: 1.34E-10; mr1804 (All); LR P-value: 3.69E-07; mr1914 (All); LR P-value: 3.53E-12; mr1946 (All); LR P-value: 1.92E-08; mr1208_2 (All); LR P-value: 1.49E-38; mr1321_2 (All); LR P-value: 1.39E-07; mr1362_2 (All); LR P-value: 6.37E-20; mr1398_2 (All); LR P-value: 1.93E-09; mr1578_2 (All); LR P-value: 4.92E-15; mr1581_2 (All); LR P-value: 2.06E-18; mr1598_2 (All); LR P-value: 1.20E-32; mr1712_2 (All); LR P-value: 2.83E-17; mr1717_2 (All); LR P-value: 1.14E-13; mr1721_2 (All); LR P-value: 5.00E-48; mr1770_2 (All); LR P-value: 6.01E-13; mr1836_2 (All); LR P-value: 2.30E-18; mr1946_2 (All); LR P-value: 3.51E-10; mr1948_2 (All); LR P-value: 3.51E-10 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33440.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.092; most accessible tissue: Zhenshan97 flower, score: 86.194 |
| vg0420224812 (J) | chr04 | 20224812 | C | A | 96.10% | 0.00% | C -> A | NA |
LOC_Os04g33440.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.311; most accessible tissue: Zhenshan97 flower, score: 85.963 |
| vg0420225040 (J) | chr04 | 20225040 | G | T | 96.10% | 0.00% | G -> T | NA |
LOC_Os04g33440.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.232; most accessible tissue: Zhenshan97 flower, score: 85.564 |
| vg0420225145 (J) | chr04 | 20225145 | T | G | 99.40% | 0.00% | T -> G | NA |
LOC_Os04g33450.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33450.3 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33440.2 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.524; most accessible tissue: Zhenshan97 flower, score: 85.314 |
| vg0420225156 (J) | chr04 | 20225156 | TG | T | 99.50% | 0.00% | TG -> T | NA |
LOC_Os04g33450.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33450.3 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33440.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.593; most accessible tissue: Zhenshan97 flower, score: 85.141 |
| vg0420225252 (J) | chr04 | 20225252 | C | G | 63.20% | 0.00% | C -> G |
mr1655 (All); LR P-value: 4.09E-14;
mr1717 (All); LR P-value: 4.93E-07; mr1770 (All); LR P-value: 9.30E-10; mr1836 (All); LR P-value: 2.84E-08; mr1946 (All); LR P-value: 2.28E-08; mr1040_2 (All); LR P-value: 1.67E-15; mr1362_2 (All); LR P-value: 1.78E-20; mr1619_2 (Ind_All); LR P-value: 8.89E-07; mr1836_2 (All); LR P-value: 7.39E-19; mr1946_2 (All); LR P-value: 3.32E-09; mr1948_2 (All); LR P-value: 3.32E-09 |
LOC_Os04g33450.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33450.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33440.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.660; most accessible tissue: Callus, score: 87.374 |
| vg0420225335 (J) | chr04 | 20225335 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33440.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 62.918; most accessible tissue: Zhenshan97 flower, score: 81.724 |
| vg0420225386 (J) | chr04 | 20225386 | C | A | 99.50% | 0.00% | C -> A | NA |
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33440.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.519; most accessible tissue: Zhenshan97 flower, score: 84.217 |
| vg0420225549 (J) | chr04 | 20225549 | T | G | 61.90% | 0.23% | G -> T |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33450.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33440.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.014; most accessible tissue: Callus, score: 87.775 |
|
| vg0420225748 (J) | chr04 | 20225748 | T | A | 99.20% | 0.00% | T -> A | NA |
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33440.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.073; most accessible tissue: Callus, score: 84.585 |
| vg0420225893 (J) | chr04 | 20225893 | A | G | 61.90% | 0.55% | G -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33440.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.527; most accessible tissue: Zhenshan97 flower, score: 87.963 |
|
| vg0420225932 (J) | chr04 | 20225932 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os04g33450.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33450.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33440.2 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.822; most accessible tissue: Zhenshan97 flower, score: 88.827 |
| vg0420225952 (J) | chr04 | 20225952 | T | C | 59.80% | 0.00% | C -> T |
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 |
LOC_Os04g33450.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33450.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33440.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.543; most accessible tissue: Zhenshan97 flower, score: 88.928 |
| vg0420225963 (J) | chr04 | 20225963 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33440.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.004; most accessible tissue: Zhenshan97 flower, score: 89.221 |
| vg0420226011 (J) | chr04 | 20226011 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os04g33450.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33450.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33440.2 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.876; most accessible tissue: Zhenshan97 flower, score: 92.719 |
| vg0420226013 (J) | chr04 | 20226013 | AGTATAA GAAGCCC | A | 99.90% | 0.00% | AGTATAAGAA GCCC -> A | NA |
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33440.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.876; most accessible tissue: Zhenshan97 flower, score: 92.719 |
| vg0420226143 (J) | chr04 | 20226143 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33440.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.890; most accessible tissue: Zhenshan97 flower, score: 94.443 |
| vg0420226286 (J) | chr04 | 20226286 | A | G | 59.80% | 0.00% | G -> 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 |
LOC_Os04g33440.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g33450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33450.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33430.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g33420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.716; most accessible tissue: Callus, score: 97.672 |
| vg0420226305 (J) | chr04 | 20226305 | T | C | 99.40% | 0.00% | T -> C | NA |
LOC_Os04g33440.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g33450.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.3 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33450.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g33430.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g33420.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 93.980; most accessible tissue: Callus, score: 97.672 |
| STR0420226126 (J) | chr04 | 20226126 | AAAAAGA AAAAGAA AAAGAGG AGC | AAAAAGA AAAAGAA AAAAAGG AGC | 98.70% | 0.00% | AAAAAGAAAA AGAAAAAGAG GAGC -> AAAAAGAAAA AGAAAAAAAG GAGC | NA |
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