65 variations found. LOC_Os05g04820 (MYB family transcription factor; putative; expressed), ranging from 2,311,395 bp to 2,315,444 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0502311937 (J) | chr05 | 2311937 | A | ATGTTTT | 78.60% | 0.00% | A -> ATGTTTT | NA |
|
| STR0502312472 (J) | chr05 | 2312472 | C | T | 97.50% | 0.00% | C -> A,T | NA |
|
| vg0502311555 (J) | chr05 | 2311555 | A | G | 95.50% | 0.00% | A -> G |
LOC_Os05g04820.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 82.473; most accessible tissue: Callus, score: 93.458 |
|
| vg0502311706 (J) | chr05 | 2311706 | C | G | 90.80% | 0.00% | C -> G | NA |
LOC_Os05g04820.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 78.467; most accessible tissue: Zhenshan97 root, score: 93.745 |
| vg0502311741 (J) | chr05 | 2311741 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os05g04820.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 78.370; most accessible tissue: Zhenshan97 root, score: 93.844 |
| vg0502311756 (J) | chr05 | 2311756 | T | A | 95.30% | 0.00% | T -> A | NA |
LOC_Os05g04820.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.755; most accessible tissue: Zhenshan97 root, score: 93.592 |
| vg0502311766 (J) | chr05 | 2311766 | TG | T | 82.30% | 0.00% | TG -> T,TGG | NA |
LOC_Os05g04820.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g04820.1 Alt: TGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.048; most accessible tissue: Zhenshan97 root, score: 93.893 |
| vg0502311851 (J) | chr05 | 2311851 | A | G | 95.30% | 0.00% | A -> G | NA |
LOC_Os05g04820.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.318; most accessible tissue: Zhenshan97 root, score: 93.592 |
| vg0502311873 (J) | chr05 | 2311873 | T | G | 99.30% | 0.00% | T -> G | NA |
LOC_Os05g04820.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 75.125; most accessible tissue: Zhenshan97 root, score: 93.096 |
| vg0502311887 (J) | chr05 | 2311887 | C | T | 95.30% | 0.00% | C -> T | NA |
LOC_Os05g04820.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.529; most accessible tissue: Zhenshan97 root, score: 92.725 |
| vg0502311933 (J) | chr05 | 2311933 | C | T | 90.40% | 0.00% | C -> T | NA |
LOC_Os05g04820.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 76.433; most accessible tissue: Zhenshan97 root, score: 92.693 |
| vg0502311937 (J) | chr05 | 2311937 | A | ATGTTTT | 82.70% | 0.00% | A -> ATGTTTT | NA |
The average chromatin accessibility score: 76.644; most accessible tissue: Zhenshan97 root, score: 92.529
|
| vg0502312041 (J) | chr05 | 2312041 | G | C | 99.30% | 0.00% | G -> C | NA |
LOC_Os05g04820.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 78.740; most accessible tissue: Callus, score: 91.965 |
| vg0502312122 (J) | chr05 | 2312122 | G | T | 90.30% | 0.00% | G -> T | NA |
LOC_Os05g04820.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 77.835; most accessible tissue: Zhenshan97 panicle, score: 89.846 |
| vg0502312147 (J) | chr05 | 2312147 | T | TGAA | 77.70% | 1.97% | T -> TGAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g04820.1 Alt: TGAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.487; most accessible tissue: Zhenshan97 panicle, score: 91.030 |
| vg0502312152 (J) | chr05 | 2312152 | A | AAGAAC | 90.50% | 0.00% | A -> AAGAAC | NA |
The average chromatin accessibility score: 80.753; most accessible tissue: Zhenshan97 panicle, score: 91.030
|
| vg0502312220 (J) | chr05 | 2312220 | T | C | 90.40% | 0.00% | T -> C | NA |
LOC_Os05g04820.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 82.757; most accessible tissue: Callus, score: 91.076 |
| vg0502312349 (J) | chr05 | 2312349 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os05g04820.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.730; most accessible tissue: Minghui63 flower, score: 93.982 |
| vg0502312372 (J) | chr05 | 2312372 | G | A | 97.80% | 0.00% | G -> A | NA |
LOC_Os05g04820.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os05g04820.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.017; most accessible tissue: Minghui63 flower, score: 94.309 |
| vg0502312447 (J) | chr05 | 2312447 | TG | T | 99.90% | 0.00% | TG -> T | NA |
LOC_Os05g04820.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 88.310; most accessible tissue: Minghui63 flower, score: 95.486 |
| vg0502312472 (J) | chr05 | 2312472 | C | A | 88.10% | 0.21% | C -> T,A | NA |
LOC_Os05g04820.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os05g04820.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os05g04820.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.739; most accessible tissue: Minghui63 flower, score: 95.380 |
| vg0502312491 (J) | chr05 | 2312491 | A | ACACAG | 90.50% | 0.00% | A -> ACACAG | NA |
The average chromatin accessibility score: 86.959; most accessible tissue: Minghui63 flower, score: 95.106
|
| vg0502312513 (J) | chr05 | 2312513 | A | C | 94.80% | 0.00% | A -> C | NA |
LOC_Os05g04820.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.180; most accessible tissue: Minghui63 flower, score: 95.286 |
| vg0502312548 (J) | chr05 | 2312548 | A | G | 58.50% | 0.00% | A -> G |
mr1030_2 (All); LR P-value: 1.01E-07;
mr1045_2 (All); LR P-value: 1.64E-06; mr1109_2 (Jap_All); LR P-value: 4.51E-07; mr1358_2 (All); LR P-value: 5.08E-07; mr1391_2 (All); LR P-value: 2.13E-06; mr1446_2 (All); LR P-value: 1.13E-07; mr1754_2 (All); LR P-value: 1.16E-07; mr1865_2 (Jap_All); LMM P-value: 4.11E-06 |
LOC_Os05g04820.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.151; most accessible tissue: Minghui63 flower, score: 95.349 |
| vg0502312601 (J) | chr05 | 2312601 | G | A | 97.80% | 0.00% | G -> A | NA |
LOC_Os05g04820.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.758; most accessible tissue: Minghui63 flower, score: 96.097 |
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