93 variations found. LOC_Os02g13830 (osFTL13 FT-Like13 homologous to Flowering Locus T gene%3B contains Pfam profile PF01161%3A Phosphatidylethanolamine-binding protein; expressed), ranging from 7,485,425 bp to 7,487,001 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 |
---|---|---|---|---|---|---|---|---|---|
STR0207486111 (J) | chr02 | 7486111 | TGTGTG | TGTGT | 91.20% | 0.00% | TGTGTG -> T,TGTGT | NA |
|
vg0207485524 (J) | chr02 | 7485524 | G | C | 50.80% | 0.00% | C -> G |
LOC_Os02g13830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.803; most accessible tissue: Callus, score: 91.599 |
|
vg0207485564 (J) | chr02 | 7485564 | G | A | 96.50% | 0.00% | G -> A |
LOC_Os02g13830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 69.565; most accessible tissue: Callus, score: 91.599 |
|
vg0207485567 (J) | chr02 | 7485567 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os02g13830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 70.206; most accessible tissue: Callus, score: 91.599 |
vg0207485568 (J) | chr02 | 7485568 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g13830.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 70.081; most accessible tissue: Callus, score: 91.599 |
vg0207485584 (J) | chr02 | 7485584 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os02g13830.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 66.055; most accessible tissue: Zhenshan97 young leaf, score: 86.698 |
vg0207485590 (J) | chr02 | 7485590 | T | C | 62.20% | 0.00% | C -> T |
mr1105 (All); LR P-value: 2.97E-35;
mr1122 (All); LR P-value: 5.71E-22; mr1168 (All); LR P-value: 5.51E-23; mr1198 (All); LR P-value: 3.61E-09; mr1302 (All); LR P-value: 1.09E-08; mr1383 (All); LR P-value: 1.11E-26; mr1488 (All); LR P-value: 6.29E-08; mr1529 (All); LR P-value: 1.47E-17; mr1557 (All); LR P-value: 2.80E-17; mr1683 (All); LR P-value: 1.25E-10; mr1779 (All); LR P-value: 1.19E-07; mr1383_2 (All); LR P-value: 1.81E-22; mr1817_2 (All); LR P-value: 1.07E-18 |
LOC_Os02g13830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.098; most accessible tissue: Zhenshan97 young leaf, score: 86.383 |
vg0207485612 (J) | chr02 | 7485612 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os02g13830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 68.252; most accessible tissue: Zhenshan97 young leaf, score: 87.443 |
vg0207485638 (J) | chr02 | 7485638 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g13830.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.958; most accessible tissue: Zhenshan97 young leaf, score: 87.859 |
vg0207485666 (J) | chr02 | 7485666 | C | T | 99.60% | 0.23% | C -> T | NA |
LOC_Os02g13830.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.841; most accessible tissue: Zhenshan97 young leaf, score: 86.698 |
vg0207485671 (J) | chr02 | 7485671 | G | A | 82.90% | 0.00% | G -> A |
mr1229 (All); LR P-value: 7.39E-07;
mr1229 (Jap_All); LR P-value: 1.65E-07; mr1315 (All); LR P-value: 1.53E-06; mr1338 (All); LR P-value: 9.37E-08; mr1405 (All); LR P-value: 4.48E-06; mr1418 (All); LR P-value: 2.43E-06; mr1506 (All); LR P-value: 7.87E-08; mr1090_2 (Jap_All); LR P-value: 2.49E-07; mr1211_2 (Jap_All); LR P-value: 5.26E-07; mr1229_2 (Jap_All); LR P-value: 9.58E-07 |
LOC_Os02g13830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.568; most accessible tissue: Zhenshan97 young leaf, score: 86.852 |
vg0207485673 (J) | chr02 | 7485673 | G | A | 98.30% | 0.00% | G -> GT,A | NA |
LOC_Os02g13830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g13830.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.627; most accessible tissue: Zhenshan97 young leaf, score: 86.852 |
vg0207485680 (J) | chr02 | 7485680 | G | A | 50.00% | 0.00% | G -> A |
LOC_Os02g13830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 73.199; most accessible tissue: Callus, score: 89.897 |
|
vg0207485689 (J) | chr02 | 7485689 | C | T | 86.20% | 0.00% | C -> T |
LOC_Os02g13830.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 74.428; most accessible tissue: Callus, score: 89.897 |
|
vg0207485724 (J) | chr02 | 7485724 | A | C | 83.30% | 0.00% | A -> C |
mr1028 (All); LR P-value: 2.46E-06;
mr1229 (All); LR P-value: 5.72E-07; mr1229 (Jap_All); LR P-value: 1.65E-07; mr1315 (All); LR P-value: 1.07E-06; mr1338 (All); LR P-value: 6.39E-08; mr1405 (All); LR P-value: 2.84E-06; mr1418 (All); LR P-value: 5.36E-07; mr1420 (All); LR P-value: 1.08E-06; mr1453 (All); LR P-value: 4.82E-07; mr1506 (All); LR P-value: 2.23E-08; mr1779 (All); LR P-value: 1.03E-07; mr1090_2 (Jap_All); LR P-value: 2.49E-07; mr1211_2 (Jap_All); LR P-value: 5.26E-07; mr1229_2 (Jap_All); LR P-value: 9.58E-07 |
LOC_Os02g13830.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 72.821; most accessible tissue: Callus, score: 89.897 |
vg0207485746 (J) | chr02 | 7485746 | A | G | 92.10% | 0.00% | A -> G | NA |
LOC_Os02g13830.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.379; most accessible tissue: Callus, score: 89.897 |
vg0207485753 (J) | chr02 | 7485753 | A | T | 87.70% | 0.00% | A -> T |
mr1084 (All); LR P-value: 5.57E-11;
mr1220 (All); LR P-value: 5.66E-07; mr1229 (All); LR P-value: 6.83E-07; mr1229 (Jap_All); LR P-value: 1.65E-07; mr1338 (All); LR P-value: 7.28E-07; mr1405 (All); LR P-value: 1.36E-07; mr1506 (All); LR P-value: 5.74E-08; mr1668 (All); LR P-value: 2.69E-07; mr1775 (All); LR P-value: 7.33E-11; mr1851 (All); LR P-value: 1.10E-06; mr1871 (All); LR P-value: 4.03E-13; mr1090_2 (Jap_All); LR P-value: 2.49E-07; mr1211_2 (Jap_All); LR P-value: 5.26E-07; mr1229_2 (Jap_All); LR P-value: 9.58E-07; mr1554_2 (All); LR P-value: 1.30E-06; mr1646_2 (All); LR P-value: 6.33E-10; mr1680_2 (All); LR P-value: 3.23E-10 |
LOC_Os02g13830.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 70.158; most accessible tissue: Callus, score: 89.897 |
vg0207485769 (J) | chr02 | 7485769 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os02g13830.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 69.249; most accessible tissue: Callus, score: 89.897 |
vg0207485840 (J) | chr02 | 7485840 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os02g13830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 69.382; most accessible tissue: Minghui63 panicle, score: 82.797 |
vg0207485848 (J) | chr02 | 7485848 | C | T | 79.30% | 0.00% | T -> C |
LOC_Os02g13830.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.698; most accessible tissue: Minghui63 panicle, score: 81.412 |
|
vg0207485857 (J) | chr02 | 7485857 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g13830.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 70.203; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
vg0207485866 (J) | chr02 | 7485866 | C | T | 99.10% | 0.00% | C -> T | NA |
LOC_Os02g13830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.913; most accessible tissue: Zhenshan97 panicle, score: 81.752 |
vg0207485902 (J) | chr02 | 7485902 | G | T | 98.60% | 0.00% | G -> T | NA |
LOC_Os02g13830.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 71.878; most accessible tissue: Minghui63 panicle, score: 83.421 |
vg0207485917 (J) | chr02 | 7485917 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os02g13830.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 73.278; most accessible tissue: Minghui63 panicle, score: 83.421 |
vg0207485991 (J) | chr02 | 7485991 | C | CACACAA ACCTA | 53.10% | 15.49% | C -> CACACAAACC TA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g13830.1 Alt: CACACAAACCTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.165; most accessible tissue: Callus, score: 94.833 |
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