11 variations found. LOC_Os07g43580 (MYB family transcription factor; putative; expressed), ranging from 26,075,298 bp to 26,077,154 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0726075728 (J) | chr07 | 26075728 | CT | C | 72.60% | 0.00% | CT -> C | NA |
LOC_Os07g43580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 75.861; most accessible tissue: Callus, score: 95.135 |
| vg0726075830 (J) | chr07 | 26075830 | T | C | 95.60% | 0.00% | T -> C | NA |
LOC_Os07g43580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 71.619; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| vg0726075952 (J) | chr07 | 26075952 | G | A | 61.10% | 0.00% | A -> G |
mr1070 (All); LR P-value: 3.63E-11;
mr1128 (All); LR P-value: 2.58E-10; mr1336 (All); LR P-value: 3.02E-11; mr1386 (All); LR P-value: 5.29E-12; mr1751 (All); LR P-value: 2.83E-11; mr1039_2 (All); LR P-value: 1.02E-27; mr1128_2 (All); LR P-value: 1.40E-15; mr1205_2 (All); LR P-value: 4.28E-07; mr1275_2 (All); LR P-value: 8.76E-07; mr1304_2 (All); LR P-value: 9.70E-23; mr1336_2 (All); LR P-value: 6.19E-19; mr1386_2 (All); LR P-value: 4.48E-23; mr1579_2 (All); LR P-value: 1.64E-15; mr1632_2 (All); LR P-value: 3.80E-32; mr1646_2 (All); LR P-value: 9.27E-10 |
LOC_Os07g43580.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.180; most accessible tissue: Zhenshan97 panicle, score: 92.904 |
| vg0726075976 (J) | chr07 | 26075976 | G | A | 74.40% | 0.00% | G -> A |
LOC_Os07g43580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.943; most accessible tissue: Zhenshan97 panicle, score: 93.351 |
|
| vg0726076016 (J) | chr07 | 26076016 | G | C | 61.00% | 0.00% | C -> G |
mr1070 (All); LR P-value: 7.46E-11;
mr1336 (All); LR P-value: 1.36E-10; mr1586 (Ind_All); LR P-value: 4.44E-06; mr1128_2 (All); LR P-value: 5.78E-15; mr1275_2 (All); LR P-value: 1.60E-06; mr1304_2 (All); LR P-value: 2.88E-22; mr1336_2 (All); LR P-value: 1.71E-18; mr1386_2 (All); LR P-value: 4.11E-23; mr1579_2 (All); LR P-value: 7.45E-15 |
LOC_Os07g43580.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.625; most accessible tissue: Zhenshan97 panicle, score: 93.558 |
| vg0726076374 (J) | chr07 | 26076374 | C | T | 77.70% | 5.73% | C -> T | NA |
LOC_Os07g43580.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g43580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 80.843; most accessible tissue: Zhenshan97 panicle, score: 95.756 |
| vg0726076735 (J) | chr07 | 26076735 | C | T | 64.30% | 0.00% | T -> C |
mr1070 (All); LR P-value: 1.53E-10;
mr1128 (All); LR P-value: 2.96E-10; mr1336 (All); LR P-value: 2.39E-09; mr1386 (All); LR P-value: 1.99E-12; mr1414 (All); LR P-value: 3.08E-27; mr1579 (All); LR P-value: 3.19E-12; mr1647 (All); LR P-value: 1.09E-33; mr1754 (All); LR P-value: 1.04E-20; mr1128_2 (All); LR P-value: 3.31E-13 |
LOC_Os07g43580.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.981; most accessible tissue: Zhenshan97 panicle, score: 95.806 |
| vg0726076849 (J) | chr07 | 26076849 | C | CAAG | 96.80% | 0.00% | C -> CAAG | NA |
The average chromatin accessibility score: 84.528; most accessible tissue: Zhenshan97 panicle, score: 96.491
|
| vg0726077039 (J) | chr07 | 26077039 | GGA | G | 64.50% | 0.00% | G -> GGA | NA |
The average chromatin accessibility score: 93.687; most accessible tissue: Zhenshan97 panicle, score: 98.337
|
| vg0726077141 (J) | chr07 | 26077141 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os07g43580.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 94.139; most accessible tissue: Zhenshan97 panicle, score: 98.929 |
| STR0726076850 (J) | chr07 | 26076850 | AAGAAGA AGAAGAA G | AAGAAGA AGAAGAA GAAG | 96.50% | 0.00% | AAGAAGAAGA AGAAG -> AAGAAGAAGA AGAAGAAG | NA |
|