9 variations found. LOC_Os04g46490 (aquaporin protein; putative; expressed), ranging from 27,575,660 bp to 27,576,996 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0427575989 (J) | chr04 | 27575989 | GCCGGCG CCGGCT | G | 99.90% | 0.00% | GCCGGCGCCG GCT -> G | NA |
LOC_Os04g46490.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os04g46480.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g46480.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.354; most accessible tissue: Zhenshan97 flower, score: 95.566 |
| vg0427576247 (J) | chr04 | 27576247 | T | C | 53.80% | 0.00% | C -> T |
LOC_Os04g46490.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.534; most accessible tissue: Zhenshan97 flower, score: 96.028 |
|
| vg0427576275 (J) | chr04 | 27576275 | G | A | 80.30% | 0.11% | G -> A |
mr1031 (Ind_All); LR P-value: 2.23E-06;
mr1035 (Ind_All); LR P-value: 5.65E-06; mr1050 (Ind_All); LR P-value: 3.36E-07; mr1174 (Ind_All); LR P-value: 3.06E-07; mr1272 (Ind_All); LR P-value: 1.28E-06; mr1291 (All); LR P-value: 1.02E-06; mr1354 (Ind_All); LR P-value: 1.20E-07; mr1387 (All); LR P-value: 9.16E-06; mr1502 (Ind_All); LR P-value: 9.26E-06; mr1626 (Ind_All); LR P-value: 1.33E-06; mr1709 (All); LR P-value: 1.22E-06; mr1709 (Ind_All); LR P-value: 1.50E-06; mr1798 (Ind_All); LR P-value: 2.60E-06; mr1035_2 (Ind_All); LMM P-value: 6.74E-06; LR P-value: 6.74E-06; mr1158_2 (All); LR P-value: 1.06E-06; mr1170_2 (All); LR P-value: 2.77E-08; mr1184_2 (All); LR P-value: 2.49E-06; mr1272_2 (Ind_All); LR P-value: 6.72E-06; mr1354_2 (Ind_All); LR P-value: 1.41E-08; mr1355_2 (Ind_All); LR P-value: 9.93E-06; mr1478_2 (Ind_All); LR P-value: 1.20E-06; mr1497_2 (All); LR P-value: 2.38E-06; mr1631_2 (Ind_All); LR P-value: 1.38E-06; mr1706_2 (All); LR P-value: 1.11E-06; mr1715_2 (Ind_All); LR P-value: 3.07E-11; mr1720_2 (Ind_All); LR P-value: 3.81E-07; mr1895_2 (Ind_All); LR P-value: 2.28E-07; mr1904_2 (Ind_All); LR P-value: 3.24E-07; mr1931_2 (All); LR P-value: 2.10E-07; mr1931_2 (Ind_All); LR P-value: 7.61E-08; mr1942_2 (Ind_All); LR P-value: 1.55E-06 |
LOC_Os04g46490.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g46490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 90.716; most accessible tissue: Zhenshan97 panicle, score: 95.602 |
| vg0427576394 (J) | chr04 | 27576394 | TGTG | T | 54.00% | 0.23% | T -> TGTG | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g46480.1 Alt: TGTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46480.2 Alt: TGTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46490.1 Alt: TGTG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.058; most accessible tissue: Zhenshan97 panicle, score: 93.657 |
| vg0427576821 (J) | chr04 | 27576821 | G | A | 97.90% | 0.00% | G -> A | NA |
LOC_Os04g46490.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.392; most accessible tissue: Zhenshan97 flower, score: 87.789 |
| vg0427576840 (J) | chr04 | 27576840 | G | A | 80.20% | 0.19% | G -> A |
mr1050 (Ind_All); LR P-value: 7.32E-07;
mr1155 (Ind_All); LR P-value: 7.61E-06; mr1174 (Ind_All); LR P-value: 1.10E-07; mr1291 (All); LR P-value: 1.27E-06; mr1354 (Ind_All); LR P-value: 5.40E-07; mr1626 (Ind_All); LR P-value: 4.06E-06; mr1709 (All); LR P-value: 4.89E-07; mr1709 (Ind_All); LR P-value: 5.50E-07; mr1798 (Ind_All); LR P-value: 1.27E-06; mr1035_2 (Ind_All); LMM P-value: 4.77E-06; LR P-value: 4.77E-06; mr1158_2 (All); LR P-value: 1.37E-06; mr1170_2 (All); LR P-value: 4.76E-08; mr1174_2 (Ind_All); LR P-value: 2.55E-07; mr1184_2 (All); LR P-value: 5.81E-06; mr1319_2 (Ind_All); LR P-value: 9.13E-06; mr1354_2 (Ind_All); LR P-value: 1.06E-08; mr1497_2 (All); LR P-value: 9.70E-06; mr1631_2 (Ind_All); LR P-value: 6.72E-07; mr1706_2 (All); LR P-value: 3.97E-06; mr1715_2 (Ind_All); LR P-value: 6.07E-12; mr1720_2 (Ind_All); LR P-value: 5.42E-07; mr1733_2 (Ind_All); LR P-value: 6.36E-06; mr1895_2 (Ind_All); LR P-value: 1.79E-07; mr1931_2 (All); LR P-value: 3.89E-07; mr1931_2 (Ind_All); LR P-value: 1.83E-07; mr1942_2 (Ind_All); LR P-value: 6.90E-06 |
LOC_Os04g46490.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g46490.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 78.316; most accessible tissue: Zhenshan97 flower, score: 88.021 |
| vg0427576881 (J) | chr04 | 27576881 | C | T | 80.20% | 0.15% | C -> T |
mr1031 (Ind_All); LR P-value: 5.33E-06;
mr1035 (Ind_All); LR P-value: 6.35E-06; mr1050 (Ind_All); LR P-value: 2.20E-07; mr1155 (Ind_All); LR P-value: 4.81E-06; mr1174 (Ind_All); LR P-value: 1.38E-07; mr1272 (Ind_All); LR P-value: 8.21E-07; mr1291 (All); LR P-value: 1.60E-06; mr1354 (Ind_All); LR P-value: 5.62E-08; mr1626 (Ind_All); LR P-value: 1.41E-06; mr1709 (All); LR P-value: 8.85E-07; mr1709 (Ind_All); LR P-value: 1.13E-06; mr1798 (Ind_All); LR P-value: 5.96E-07; mr1935 (Ind_All); LR P-value: 6.94E-09; mr1035_2 (Ind_All); LMM P-value: 5.11E-06; LR P-value: 5.11E-06; mr1158_2 (All); LR P-value: 6.09E-07; mr1170_2 (All); LR P-value: 5.67E-08; mr1174_2 (Ind_All); LR P-value: 2.48E-07; mr1184_2 (All); LR P-value: 3.64E-06; mr1272_2 (Ind_All); LR P-value: 6.00E-06; mr1354_2 (Ind_All); LR P-value: 7.98E-09; mr1478_2 (Ind_All); LR P-value: 1.88E-06; mr1497_2 (All); LR P-value: 4.96E-06; mr1631_2 (Ind_All); LR P-value: 1.25E-06; mr1706_2 (All); LR P-value: 2.21E-06; mr1715_2 (Ind_All); LR P-value: 8.55E-12; mr1720_2 (Ind_All); LR P-value: 2.35E-07; mr1733_2 (Ind_All); LR P-value: 4.61E-06; mr1895_2 (Ind_All); LR P-value: 3.86E-07; mr1904_2 (Ind_All); LR P-value: 4.71E-07; mr1931_2 (All); LR P-value: 3.55E-07; mr1931_2 (Ind_All); LR P-value: 1.71E-07; mr1942_2 (Ind_All); LR P-value: 1.27E-06 |
LOC_Os04g46490.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g46490.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 77.644; most accessible tissue: Zhenshan97 flower, score: 87.671 |
| vg0427576927 (J) | chr04 | 27576927 | T | A | 99.60% | 0.00% | T -> A | NA |
LOC_Os04g46490.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g46480.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46480.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.480; most accessible tissue: Zhenshan97 flower, score: 87.848 |
| vg0427576932 (J) | chr04 | 27576932 | CTGTG | CTG | 52.90% | 0.40% | CTG -> CTGTG,C,CT GTGTG | NA |
LOC_Os04g46490.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g46480.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g46480.2 Alt: C| upstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os04g46490.1 Alt: CTGTG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46480.1 Alt: CTGTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46480.2 Alt: CTGTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46490.1 Alt: CTGTGTG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46480.1 Alt: CTGTGTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g46480.2 Alt: CTGTGTG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.784; most accessible tissue: Zhenshan97 flower, score: 87.906 |