13 variations found. LOC_Os09g32030 (expressed protein), ranging from 19,119,276 bp to 19,121,242 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0919119302 (J) | chr09 | 19119302 | G | T | 42.40% | 0.00% | T -> G,A | NA |
LOC_Os09g32030.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g32020.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32025.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32040.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32030.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32020.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32025.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.298; most accessible tissue: Minghui63 panicle, score: 97.163 |
| vg0919119487 (J) | chr09 | 19119487 | T | C | 65.20% | 0.32% | C -> T |
mr1008 (All); LR P-value: 2.45E-105;
mr1009 (All); LR P-value: 2.31E-102; mr1172 (All); LR P-value: 9.79E-11; mr1518 (All); LR P-value: 3.70E-23; mr1518 (Ind_All); LR P-value: 2.73E-09; mr1542 (All); LR P-value: 1.93E-35; mr1546 (All); LR P-value: 1.69E-28; mr1676 (All); LR P-value: 3.23E-24; mr1676 (Ind_All); LR P-value: 1.86E-09; mr1719 (All); LR P-value: 1.77E-36; mr1874 (All); LR P-value: 1.24E-13; mr1889 (All); LR P-value: 1.15E-52; mr1299_2 (All); LR P-value: 6.01E-08; mr1342_2 (All); LR P-value: 1.16E-17; mr1403_2 (All); LR P-value: 3.01E-25; mr1486_2 (All); LR P-value: 1.01E-45; mr1546_2 (All); LR P-value: 3.44E-49; mr1637_2 (All); LR P-value: 3.05E-19; mr1676_2 (All); LR P-value: 1.45E-26; mr1676_2 (Ind_All); LR P-value: 1.98E-10; mr1700_2 (All); LR P-value: 9.32E-08 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g32030.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32020.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32025.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32040.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.151; most accessible tissue: Minghui63 flower, score: 92.540 |
| vg0919119560 (J) | chr09 | 19119560 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os09g32030.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os09g32020.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g32025.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g32040.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.015; most accessible tissue: Minghui63 flower, score: 91.905 |
| vg0919119587 (J) | chr09 | 19119587 | C | T | 65.10% | 0.32% | T -> C |
mr1008 (All); LR P-value: 2.37E-104;
mr1009 (All); LR P-value: 3.29E-101; mr1172 (All); LR P-value: 8.62E-11; mr1518 (All); LR P-value: 4.29E-23; mr1518 (Ind_All); LR P-value: 2.73E-09; mr1542 (All); LR P-value: 1.52E-35; mr1546 (All); LR P-value: 2.47E-28; mr1676 (All); LR P-value: 4.80E-24; mr1676 (Ind_All); LR P-value: 1.86E-09; mr1874 (All); LR P-value: 1.75E-13; mr1889 (All); LR P-value: 1.04E-53; mr1896 (All); LR P-value: 3.00E-68; mr1342_2 (All); LR P-value: 1.03E-17; mr1403_2 (All); LR P-value: 3.77E-25; mr1486_2 (All); LR P-value: 4.41E-46; mr1546_2 (All); LR P-value: 2.11E-49; mr1637_2 (All); LR P-value: 3.49E-19; mr1676_2 (All); LR P-value: 3.02E-26; mr1676_2 (Ind_All); LR P-value: 1.98E-10 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g32030.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32020.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32025.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32040.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.153; most accessible tissue: Minghui63 flower, score: 91.761 |
| vg0919119852 (J) | chr09 | 19119852 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os09g32030.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os09g32020.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g32025.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g32040.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.101; most accessible tissue: Zhenshan97 panicle, score: 79.799 |
| vg0919119943 (J) | chr09 | 19119943 | G | A | 77.70% | 0.00% | G -> A | NA |
LOC_Os09g32020.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g32025.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32030.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.445; most accessible tissue: Zhenshan97 panicle, score: 78.302 |
| vg0919120357 (J) | chr09 | 19120357 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os09g32030.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.020; most accessible tissue: Minghui63 flower, score: 73.172 |
| vg0919120424 (J) | chr09 | 19120424 | GA | G | 98.00% | 0.00% | GA -> G | NA |
LOC_Os09g32020.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g32025.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32040.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32050.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32050.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32030.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.610; most accessible tissue: Minghui63 flower, score: 75.455 |
| vg0919120663 (J) | chr09 | 19120663 | AAG | A | 74.50% | 0.00% | A -> AAG | NA |
LOC_Os09g32020.1 Alt: AAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g32025.1 Alt: AAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32040.1 Alt: AAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32050.1 Alt: AAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32050.2 Alt: AAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32030.1 Alt: AAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.807; most accessible tissue: Minghui63 flower, score: 91.576 |
| vg0919120716 (J) | chr09 | 19120716 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os09g32030.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.396; most accessible tissue: Minghui63 flower, score: 91.689 |
| vg0919120959 (J) | chr09 | 19120959 | G | A | 62.80% | 0.00% | A -> G |
mr1146 (All); LR P-value: 1.27E-14;
mr1518 (All); LR P-value: 3.71E-19; mr1299_2 (All); LR P-value: 4.17E-08; mr1403_2 (All); LR P-value: 6.49E-24; mr1623_2 (All); LR P-value: 1.91E-07; mr1637_2 (All); LR P-value: 6.44E-19; mr1676_2 (All); LR P-value: 3.44E-21; mr1676_2 (Ind_All); LR P-value: 9.00E-06; mr1700_2 (All); LR P-value: 5.23E-08 |
LOC_Os09g32030.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.719; most accessible tissue: Zhenshan97 panicle, score: 96.375 |
| vg0919121221 (J) | chr09 | 19121221 | A | G | 62.80% | 0.00% | G -> A |
mr1172 (All); LR P-value: 1.28E-10;
mr1325 (All); LR P-value: 1.19E-10; mr1326 (All); LR P-value: 1.16E-12; mr1518 (All); LR P-value: 3.70E-19; mr1277_2 (Ind_All); LR P-value: 5.10E-06; mr1623_2 (All); LR P-value: 4.09E-07; mr1637_2 (All); LR P-value: 4.18E-19; mr1676_2 (All); LR P-value: 7.59E-21; mr1676_2 (Ind_All); LR P-value: 5.46E-06; mr1700_2 (All); LR P-value: 9.82E-08 |
LOC_Os09g32030.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g32020.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32025.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32050.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g32050.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.196; most accessible tissue: Callus, score: 98.582 |
| STR0919120956 (J) | chr09 | 19120956 | GGGGGGG AGCGCGT | GGGAGGG AGCGCGT | 53.60% | 0.00% | GGGAGGGAGC GCGT -> GGGGGGGAGC GCGT | NA |
|