9 variations found. Os02g0785000/LOC_Os02g54370 (hypro1; putative; expressed), ranging from 33,324,527 bp to 33,325,924 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g54370 | hypro1, putative, expressed; RAP ID: Os02g0785000; MSU ID: LOC_Os02g54370 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233324638 (J) | chr02 | 33324638 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os02g54370.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54360.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.260; most accessible tissue: Zhenshan97 root, score: 68.908 |
| vg0233324652 (J) | chr02 | 33324652 | T | A | 56.10% | 0.00% | A -> T,AT |
mr1047 (All); LR P-value: 1.11E-08;
mr1164 (All); LR P-value: 2.63E-15; mr1379 (All); LR P-value: 6.35E-10; mr1559 (All); LR P-value: 5.15E-08; mr1580 (All); LR P-value: 1.14E-20; mr1825 (All); LR P-value: 3.85E-17; mr1084_2 (All); LR P-value: 2.68E-08; mr1133_2 (All); LR P-value: 6.35E-15; mr1148_2 (All); LR P-value: 2.39E-15; mr1198_2 (All); LR P-value: 3.96E-10; mr1205_2 (All); LR P-value: 1.85E-07; mr1227_2 (All); LR P-value: 2.12E-06; mr1228_2 (All); LR P-value: 2.30E-11; mr1548_2 (All); LR P-value: 1.01E-06; mr1558_2 (All); LR P-value: 1.73E-57; mr1571_2 (All); LR P-value: 5.36E-33; mr1575_2 (All); LR P-value: 7.64E-14; mr1579_2 (All); LR P-value: 2.27E-14; mr1580_2 (All); LR P-value: 9.03E-34; mr1646_2 (All); LR P-value: 9.60E-10; mr1677_2 (All); LR P-value: 7.37E-06; mr1680_2 (All); LR P-value: 2.07E-10; mr1686_2 (All); LR P-value: 4.42E-15; mr1698_2 (All); LR P-value: 1.18E-22; mr1825_2 (All); LR P-value: 2.51E-33; mr1922_2 (All); LR P-value: 7.50E-22; mr1924_2 (All); LR P-value: 2.08E-22; mr1940_2 (All); LR P-value: 1.43E-09; mr1950_2 (All); LR P-value: 5.77E-15 |
LOC_Os02g54370.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54360.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54370.1 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54350.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54360.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.107; most accessible tissue: Zhenshan97 root, score: 71.691 |
| vg0233324706 (J) | chr02 | 33324706 | G | T | 51.80% | 0.00% | G -> T |
mr1026 (All); LR P-value: 8.41E-33;
mr1047 (All); LR P-value: 7.95E-09; mr1063 (All); LR P-value: 1.94E-51; mr1065 (All); LR P-value: 3.33E-54; mr1078 (All); LR P-value: 6.09E-50; mr1091 (All); LR P-value: 1.77E-38; mr1108 (All); LR P-value: 8.33E-46; mr1110 (All); LR P-value: 2.87E-35; mr1112 (All); LR P-value: 4.23E-45; mr1144 (All); LR P-value: 1.35E-42; mr1161 (All); LR P-value: 3.31E-33; mr1200 (All); LR P-value: 4.20E-46; mr1208 (All); LR P-value: 3.69E-29; mr1234 (All); LR P-value: 4.52E-46; mr1237 (All); LR P-value: 3.06E-33; mr1260 (All); LR P-value: 3.03E-08; mr1261 (All); LR P-value: 1.15E-14; mr1352 (All); LR P-value: 1.49E-09; mr1580 (All); LR P-value: 1.24E-19; mr1657 (All); LR P-value: 5.10E-12; mr1870 (All); LR P-value: 4.28E-16; mr1063_2 (All); LR P-value: 8.14E-55; mr1065_2 (All); LR P-value: 3.44E-63; mr1078_2 (All); LR P-value: 4.15E-63; mr1091_2 (All); LR P-value: 1.48E-48; mr1108_2 (All); LR P-value: 1.95E-56; mr1110_2 (All); LR P-value: 2.06E-38; mr1112_2 (All); LR P-value: 3.26E-61; mr1144_2 (All); LR P-value: 2.37E-51; mr1161_2 (All); LR P-value: 1.93E-33; mr1164_2 (All); LR P-value: 5.07E-21; mr1189_2 (All); LR P-value: 3.77E-12; mr1228_2 (All); LR P-value: 6.27E-10; mr1234_2 (All); LR P-value: 5.36E-59; mr1260_2 (All); LR P-value: 1.27E-19; mr1323_2 (All); LR P-value: 8.39E-26; mr1531_2 (All); LR P-value: 2.86E-19; mr1580_2 (All); LR P-value: 7.00E-33; mr1728_2 (All); LR P-value: 4.30E-11; mr1734_2 (All); LR P-value: 1.70E-11; mr1825_2 (All); LR P-value: 1.43E-32; mr1870_2 (All); LR P-value: 8.69E-19 |
LOC_Os02g54370.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54360.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.826; most accessible tissue: Zhenshan97 root, score: 75.275 |
| vg0233325181 (J) | chr02 | 33325181 | G | A | 94.00% | 0.00% | G -> A |
LOC_Os02g54370.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.960; most accessible tissue: Zhenshan97 young leaf, score: 84.814 |
|
| vg0233325660 (J) | chr02 | 33325660 | G | A | 98.10% | 0.00% | G -> A | NA |
LOC_Os02g54370.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 61.786; most accessible tissue: Zhenshan97 root, score: 74.466 |
| vg0233325754 (J) | chr02 | 33325754 | GTCGTCG TCGTCT | G | 99.90% | 0.00% | GTCGTCGTCG TCT -> G | NA |
LOC_Os02g54370.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os02g54360.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54390.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.002; most accessible tissue: Callus, score: 81.364 |
| vg0233325810 (J) | chr02 | 33325810 | C | G | 94.00% | 0.00% | C -> G | NA |
LOC_Os02g54370.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 67.467; most accessible tissue: Zhenshan97 root, score: 82.361 |
| STR0233324651 (J) | chr02 | 33324651 | AT | AA | 55.20% | 0.00% | AA -> AT | NA |
|
| STR0233325178 (J) | chr02 | 33325178 | GTCGT | GTCAT | 96.00% | 0.00% | GTCGT -> GTCAT | NA |
|