16 variations found. LOC_Os02g51670 (ethylene-responsive transcription factor; putative; expressed), ranging from 31,648,467 bp to 31,650,538 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0231648508 (J) | chr02 | 31648508 | CATCCCA TCCCA | CATCCCA TCCCATC CCA | 62.70% | 0.00% | CATCCCATCC CATCCCA -> CATCCCATCC CA | NA |
|
| STR0231648550 (J) | chr02 | 31648550 | AG | AA | 62.80% | 0.00% | AA -> AG | NA |
|
| STR0231650226 (J) | chr02 | 31650226 | AGTAGTA GTAAGGT | AGTAGTA ATAAGGT | 48.30% | 0.00% | AGTAGTAGTA AGGT -> AGTAGTAATA AGGT | NA |
|
| vg0231648507 (J) | chr02 | 31648507 | A | ACATCC | 62.80% | 0.00% | ACATCC -> A | NA |
LOC_Os02g51670.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.109; most accessible tissue: Minghui63 flower, score: 99.835 |
| vg0231648551 (J) | chr02 | 31648551 | G | A | 64.30% | 0.00% | A -> G | NA |
LOC_Os02g51670.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 99.134; most accessible tissue: Minghui63 flower, score: 99.858 |
| vg0231648928 (J) | chr02 | 31648928 | T | C | 99.40% | 0.00% | T -> C | NA |
LOC_Os02g51670.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 91.134; most accessible tissue: Minghui63 flag leaf, score: 99.075 |
| vg0231649432 (J) | chr02 | 31649432 | C | A | 97.70% | 0.00% | C -> A | NA |
LOC_Os02g51670.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.403; most accessible tissue: Minghui63 flag leaf, score: 99.445 |
| vg0231649597 (J) | chr02 | 31649597 | C | T | 98.50% | 0.00% | C -> T | NA |
LOC_Os02g51670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.703; most accessible tissue: Minghui63 flag leaf, score: 99.457 |
| vg0231649911 (J) | chr02 | 31649911 | T | C | 54.40% | 0.00% | C -> T |
LOC_Os02g51670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.316; most accessible tissue: Minghui63 flag leaf, score: 99.337 |
|
| vg0231650032 (J) | chr02 | 31650032 | C | T | 89.30% | 0.00% | C -> T |
LOC_Os02g51670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 97.761; most accessible tissue: Minghui63 flag leaf, score: 99.331 |
|
| vg0231650071 (J) | chr02 | 31650071 | G | C | 92.70% | 0.00% | G -> C | NA |
LOC_Os02g51670.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.652; most accessible tissue: Minghui63 flag leaf, score: 99.237 |
| vg0231650106 (J) | chr02 | 31650106 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g51670.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 97.269; most accessible tissue: Minghui63 flag leaf, score: 99.194 |
| vg0231650122 (J) | chr02 | 31650122 | C | T | 95.10% | 0.00% | C -> T |
mr1114 (Jap_All); LR P-value: 9.87E-06;
mr1117 (Jap_All); LR P-value: 5.20E-07; mr1118 (Jap_All); LR P-value: 3.65E-08; mr1119 (Jap_All); LR P-value: 1.16E-06; mr1123 (Jap_All); LR P-value: 8.61E-07; mr1242 (Jap_All); LR P-value: 3.52E-07; mr1495 (Jap_All); LR P-value: 5.85E-06; mr1496 (Jap_All); LR P-value: 2.53E-07; mr1113_2 (Jap_All); LMM P-value: 1.85E-07; LR P-value: 1.04E-10; mr1114_2 (Jap_All); LR P-value: 1.89E-07; mr1117_2 (Jap_All); LR P-value: 6.67E-09; mr1118_2 (Jap_All); LR P-value: 1.75E-09; mr1119_2 (Jap_All); LR P-value: 9.11E-09; mr1120_2 (Jap_All); LR P-value: 2.14E-07; mr1123_2 (Jap_All); LR P-value: 3.95E-08; mr1183_2 (Jap_All); LR P-value: 1.71E-06; mr1240_2 (Jap_All); LR P-value: 1.07E-09; mr1242_2 (Jap_All); LR P-value: 2.76E-08; mr1247_2 (Jap_All); LR P-value: 3.18E-07; mr1495_2 (Jap_All); LR P-value: 1.31E-08; mr1496_2 (Jap_All); LR P-value: 5.19E-11; mr1936_2 (Jap_All); LR P-value: 7.91E-06 |
LOC_Os02g51670.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.062; most accessible tissue: Minghui63 flag leaf, score: 99.114 |
| vg0231650199 (J) | chr02 | 31650199 | G | A | 89.30% | 0.00% | G -> A |
LOC_Os02g51670.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.847; most accessible tissue: Minghui63 flag leaf, score: 99.132 |
|
| vg0231650233 (J) | chr02 | 31650233 | G | A | 56.40% | 0.00% | G -> A |
Grain_thickness (Ind_All); LR P-value: 1.74E-09;
mr1598 (All); LR P-value: 2.23E-19; mr1712 (All); LR P-value: 1.42E-10; mr1717 (All); LR P-value: 1.17E-08; mr1770 (All); LR P-value: 1.20E-09; mr1946 (All); LR P-value: 5.33E-09; mr1123_2 (Ind_All); LR P-value: 8.53E-07; mr1272_2 (All); LR P-value: 7.71E-07; mr1478_2 (All); LR P-value: 1.54E-08; mr1531_2 (All); LR P-value: 2.32E-22; mr1717_2 (All); LR P-value: 1.38E-12; mr1722_2 (Ind_All); LMM P-value: 2.03E-06; LR P-value: 8.12E-09; mr1728_2 (All); LR P-value: 2.00E-13; mr1835_2 (All); LR P-value: 6.99E-09; mr1860_2 (All); LR P-value: 1.27E-08; mr1904_2 (All); LR P-value: 1.42E-12; mr1904_2 (Ind_All); LR P-value: 2.54E-07; mr1910_2 (All); LR P-value: 3.63E-07; mr1936_2 (Ind_All); LR P-value: 4.58E-07; mr1946_2 (All); LR P-value: 6.67E-09; mr1948_2 (All); LR P-value: 6.67E-09 |
LOC_Os02g51670.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 97.964; most accessible tissue: Minghui63 flag leaf, score: 99.196 |
| vg0231650424 (J) | chr02 | 31650424 | TATG | T | 64.30% | 0.02% | T -> TATG | NA |
LOC_Os02g51670.1 Alt: TATG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 97.528; most accessible tissue: Minghui63 flag leaf, score: 99.440 |
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