11 variations found. LOC_Os04g49260 (heavy metal-associated domain containing protein; expressed), ranging from 29,408,861 bp to 29,409,617 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0429408874 (J) | chr04 | 29408874 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os04g49260.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g49270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.092; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0429408876 (J) | chr04 | 29408876 | C | A | 89.90% | 0.00% | C -> A | NA |
LOC_Os04g49260.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g49270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.055; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0429409018 (J) | chr04 | 29409018 | C | T | 95.30% | 0.00% | C -> T |
LOC_Os04g49260.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g49270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.121; most accessible tissue: Zhenshan97 panicle, score: 94.811 |
|
| vg0429409042 (J) | chr04 | 29409042 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g49260.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g49270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.004; most accessible tissue: Zhenshan97 panicle, score: 95.081 |
| vg0429409127 (J) | chr04 | 29409127 | C | G | 99.50% | 0.00% | C -> G | NA |
LOC_Os04g49260.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.665; most accessible tissue: Minghui63 panicle, score: 93.837 |
| vg0429409176 (J) | chr04 | 29409176 | G | T | 92.50% | 0.00% | G -> T | NA |
LOC_Os04g49260.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.212; most accessible tissue: Minghui63 panicle, score: 93.294 |
| vg0429409271 (J) | chr04 | 29409271 | G | C | 98.30% | 0.00% | G -> C | NA |
LOC_Os04g49260.1 Alt: C| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 87.790; most accessible tissue: Minghui63 panicle, score: 94.033 |
| vg0429409312 (J) | chr04 | 29409312 | A | G | 89.90% | 0.00% | A -> G | NA |
LOC_Os04g49270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g49260.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.088; most accessible tissue: Minghui63 panicle, score: 94.218 |
| vg0429409315 (J) | chr04 | 29409315 | G | A | 60.50% | 0.08% | A -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g49270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g49260.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.123; most accessible tissue: Minghui63 panicle, score: 94.218 |
|
| vg0429409436 (J) | chr04 | 29409436 | T | C | 53.90% | 0.34% | T -> C |
mr1076 (All); LR P-value: 5.54E-27;
mr1131 (All); LR P-value: 4.43E-20; mr1156 (All); LR P-value: 6.02E-15; mr1169 (All); LR P-value: 2.28E-12; mr1179 (All); LR P-value: 2.90E-18; mr1199 (All); LR P-value: 7.39E-16; mr1204 (All); LR P-value: 8.72E-30; mr1237 (All); LR P-value: 2.11E-31; mr1244 (All); LR P-value: 1.26E-21; mr1404 (All); LR P-value: 9.75E-34; mr1713 (All); LR P-value: 3.33E-11; mr1938 (All); LR P-value: 3.02E-11; mr1970 (All); LR P-value: 4.72E-64; mr1973 (All); LR P-value: 7.27E-80; mr1131_2 (All); LR P-value: 1.31E-18; mr1147_2 (All); LR P-value: 6.27E-13; mr1199_2 (All); LR P-value: 1.19E-17; mr1244_2 (All); LR P-value: 4.74E-27; mr1571_2 (All); LR P-value: 8.75E-32; mr1970_2 (All); LR P-value: 1.59E-66; mr1970_2 (Ind_All); LR P-value: 1.68E-06; mr1973_2 (All); LR P-value: 1.07E-95; mr1973_2 (Ind_All); LR P-value: 9.90E-07 |
LOC_Os04g49260.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os04g49270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 87.912; most accessible tissue: Minghui63 panicle, score: 95.014 |
| vg0429409611 (J) | chr04 | 29409611 | T | G | 95.60% | 0.00% | T -> G | NA |
LOC_Os04g49260.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g49270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.006; most accessible tissue: Minghui63 panicle, score: 96.769 |