11 variations found. LOC_Os09g29830 (helix-loop-helix DNA-binding domain containing protein; expressed), ranging from 18,141,108 bp to 18,144,524 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0918141124 (J) | chr09 | 18141124 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os09g29830.1 Alt: G| start_lost HIGH(snpEff)
LOC_Os09g29830.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29830.3 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.186; most accessible tissue: Callus, score: 96.360 |
| vg0918141368 (J) | chr09 | 18141368 | G | A | 57.60% | 0.00% | G -> A |
mr1034 (All); LR P-value: 2.68E-12;
mr1138 (All); LR P-value: 1.79E-15; mr1138 (Ind_All); LR P-value: 8.55E-09; mr1716 (All); LR P-value: 2.23E-07; mr1728 (Ind_All); LR P-value: 1.04E-07; mr1860 (Ind_All); LR P-value: 8.92E-07; mr1138_2 (All); LR P-value: 4.17E-15; mr1138_2 (Ind_All); LR P-value: 3.59E-08; mr1319_2 (All); LR P-value: 1.66E-08; mr1330_2 (All); LR P-value: 5.82E-14; mr1352_2 (All); LR P-value: 4.12E-17; mr1454_2 (All); LR P-value: 1.11E-13; mr1527_2 (All); LR P-value: 9.55E-09; mr1659_2 (All); LR P-value: 5.31E-08; mr1728_2 (Ind_All); LR P-value: 5.55E-08; mr1834_2 (All); LR P-value: 1.16E-06; mr1860_2 (Ind_All); LR P-value: 1.55E-06 |
LOC_Os09g29830.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29830.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29825.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.454; most accessible tissue: Callus, score: 99.065 |
| vg0918141621 (J) | chr09 | 18141621 | TCTC | T | 61.80% | 0.02% | T -> TCTC,TCTCC TCCTC,TCTC CTC | NA |
LOC_Os09g29830.2 Alt: TCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29830.3 Alt: TCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.1 Alt: TCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os09g29830.2 Alt: TCTCCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.3 Alt: TCTCCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.1 Alt: TCTCCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.2 Alt: TCTCCTCCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.3 Alt: TCTCCTCCTC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.1 Alt: TCTCCTCCTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.683; most accessible tissue: Zhenshan97 flower, score: 94.508 |
| vg0918141933 (J) | chr09 | 18141933 | G | T | 99.10% | 0.00% | G -> T | NA |
LOC_Os09g29830.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os09g29830.2 Alt: T| missense_variant MODERATE(snpEff) LOC_Os09g29830.3 Alt: T| missense_variant MODERATE(snpEff) The average chromatin accessibility score: 84.889; most accessible tissue: Zhenshan97 flower, score: 91.224 |
| vg0918141977 (J) | chr09 | 18141977 | A | G | 63.70% | 0.00% | G -> A |
mr1219 (Ind_All); LR P-value: 4.47E-07;
mr1274 (Ind_All); LR P-value: 9.68E-07; mr1097_2 (All); LR P-value: 2.26E-11; mr1201_2 (Ind_All); LR P-value: 9.20E-07; mr1219_2 (Ind_All); LR P-value: 8.56E-10; mr1274_2 (Ind_All); LR P-value: 1.38E-06; mr1636_2 (All); LR P-value: 8.35E-12; mr1637_2 (All); LR P-value: 2.52E-19; mr1838_2 (All); LR P-value: 2.70E-13 |
LOC_Os09g29830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g29830.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os09g29830.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 85.647; most accessible tissue: Zhenshan97 flower, score: 91.640 |
| vg0918142019 (J) | chr09 | 18142019 | T | C | 62.90% | 0.00% | C -> T |
LOC_Os09g29830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g29830.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os09g29830.3 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 84.685; most accessible tissue: Zhenshan97 flower, score: 90.278 |
|
| vg0918142196 (J) | chr09 | 18142196 | A | G | 63.70% | 0.15% | G -> A |
mr1219 (Ind_All); LR P-value: 4.47E-07;
mr1274 (Ind_All); LR P-value: 9.68E-07; mr1097_2 (All); LR P-value: 1.18E-11; mr1201_2 (Ind_All); LR P-value: 9.20E-07; mr1219_2 (Ind_All); LR P-value: 8.56E-10; mr1274_2 (Ind_All); LR P-value: 1.38E-06; mr1636_2 (All); LR P-value: 4.12E-12; mr1637_2 (All); LR P-value: 7.93E-19; mr1838_2 (All); LR P-value: 6.43E-14 |
LOC_Os09g29830.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g29830.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os09g29830.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os09g29830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os09g29830.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os09g29830.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 81.849; most accessible tissue: Minghui63 flag leaf, score: 88.103 |
| vg0918142315 (J) | chr09 | 18142315 | G | A | 97.20% | 0.00% | G -> A | NA |
LOC_Os09g29830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g29830.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os09g29830.3 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 78.413; most accessible tissue: Minghui63 flag leaf, score: 87.854 |
| vg0918142585 (J) | chr09 | 18142585 | C | A | 57.50% | 0.13% | C -> A |
mr1034 (All); LR P-value: 1.54E-12;
mr1138 (All); LR P-value: 2.20E-15; mr1138 (Ind_All); LR P-value: 1.26E-08; mr1716 (All); LR P-value: 3.22E-07; mr1728 (Ind_All); LR P-value: 1.93E-07; mr1860 (Ind_All); LR P-value: 8.55E-07; mr1138_2 (All); LR P-value: 5.30E-15; mr1138_2 (Ind_All); LR P-value: 5.53E-08; mr1330_2 (All); LR P-value: 6.17E-14; mr1352_2 (All); LR P-value: 1.58E-17; mr1527_2 (All); LR P-value: 2.80E-08; mr1659_2 (All); LR P-value: 4.01E-08; mr1728_2 (Ind_All); LR P-value: 9.43E-08; mr1834_2 (All); LR P-value: 1.67E-06; mr1860_2 (Ind_All); LR P-value: 1.54E-06 |
LOC_Os09g29830.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g29830.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os09g29830.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os09g29830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os09g29830.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os09g29830.3 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 69.927; most accessible tissue: Minghui63 flag leaf, score: 85.151 |
| vg0918143673 (J) | chr09 | 18143673 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os09g29830.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29830.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.3 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.567; most accessible tissue: Callus, score: 97.227 |
| vg0918144487 (J) | chr09 | 18144487 | A | G | 63.60% | 0.00% | G -> A |
LOC_Os09g29830.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29830.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29830.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.648; most accessible tissue: Zhenshan97 flower, score: 91.821 |
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