15 variations found. Os07g0671200/LOC_Os07g47470 (pentatricopeptide; putative; expressed), ranging from 28,373,367 bp to 28,375,023 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os07g47470 | pentatricopeptide, putative; RAP ID: Os07g0671200; MSU ID: LOC_Os07g47470 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0728373683 (J) | chr07 | 28373683 | C | A | 75.40% | 0.04% | A -> C |
Plant_height (Jap_All); LR P-value: 4.41E-15;
mr1013 (All); LR P-value: 4.78E-13; mr1045 (All); LR P-value: 2.35E-10; mr1053 (All); LR P-value: 1.46E-09; mr1056 (All); LR P-value: 1.18E-12; mr1147 (All); LR P-value: 3.35E-16; mr1164 (Jap_All); LR P-value: 2.83E-06; mr1169 (All); LR P-value: 1.33E-14; mr1180 (Jap_All); LR P-value: 1.12E-06; mr1183 (Jap_All); LR P-value: 4.16E-09; mr1229 (All); LR P-value: 7.05E-07; mr1280 (All); LR P-value: 6.08E-06; mr1283 (All); LR P-value: 2.81E-06; mr1321 (All); LR P-value: 8.08E-08; mr1380 (All); LR P-value: 9.46E-06; mr1432 (All); LR P-value: 4.13E-06; mr1503 (Jap_All); LR P-value: 1.78E-08; mr1521 (Jap_All); LR P-value: 2.18E-06; mr1614 (All); LR P-value: 1.07E-06; mr1621 (All); LR P-value: 2.28E-06; mr1748 (All); LR P-value: 4.96E-08; mr1763 (All); LR P-value: 2.81E-11; mr1826 (All); LR P-value: 5.63E-07; mr1941 (All); LR P-value: 3.70E-06; mr1011_2 (All); LR P-value: 3.47E-10; mr1011_2 (Jap_All); LR P-value: 2.15E-06; mr1180_2 (Jap_All); LR P-value: 5.28E-08; mr1709_2 (Jap_All); LR P-value: 7.55E-08; mr1860_2 (All); LR P-value: 6.50E-09; mr1940_2 (All); LR P-value: 2.50E-08 |
LOC_Os07g47470.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g47470.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 81.415; most accessible tissue: Zhenshan97 root, score: 85.796 |
| vg0728373842 (J) | chr07 | 28373842 | C | G | 99.80% | 0.00% | C -> G | NA |
LOC_Os07g47470.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os07g47460.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.054; most accessible tissue: Zhenshan97 young leaf, score: 83.623 |
| vg0728373894 (J) | chr07 | 28373894 | C | T | 95.10% | 0.00% | C -> T |
LOC_Os07g47470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 77.215; most accessible tissue: Zhenshan97 young leaf, score: 85.364 |
|
| vg0728373927 (J) | chr07 | 28373927 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os07g47470.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g47460.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.727; most accessible tissue: Zhenshan97 young leaf, score: 88.259 |
| vg0728373980 (J) | chr07 | 28373980 | G | A | 95.10% | 0.00% | G -> A | NA |
LOC_Os07g47470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.059; most accessible tissue: Zhenshan97 young leaf, score: 89.112 |
| vg0728374015 (J) | chr07 | 28374015 | C | A | 95.10% | 0.00% | C -> A | NA |
LOC_Os07g47470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.922; most accessible tissue: Zhenshan97 young leaf, score: 89.226 |
| vg0728374035 (J) | chr07 | 28374035 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os07g47470.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g47460.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.368; most accessible tissue: Zhenshan97 young leaf, score: 89.339 |
| vg0728374173 (J) | chr07 | 28374173 | T | C | 94.00% | 0.00% | T -> C |
LOC_Os07g47470.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.974; most accessible tissue: Zhenshan97 young leaf, score: 89.226 |
|
| vg0728374544 (J) | chr07 | 28374544 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os07g47470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.532; most accessible tissue: Zhenshan97 flag leaf, score: 98.432 |
| vg0728374700 (J) | chr07 | 28374700 | G | T | 95.10% | 0.00% | G -> T |
LOC_Os07g47470.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.814; most accessible tissue: Zhenshan97 flag leaf, score: 98.917 |
|
| vg0728374769 (J) | chr07 | 28374769 | C | A | 95.10% | 0.00% | C -> A |
LOC_Os07g47470.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.370; most accessible tissue: Zhenshan97 flag leaf, score: 98.378 |
|
| vg0728374778 (J) | chr07 | 28374778 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os07g47470.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os07g47460.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.357; most accessible tissue: Zhenshan97 flag leaf, score: 98.332 |
| vg0728374877 (J) | chr07 | 28374877 | C | T | 95.10% | 0.00% | C -> T | NA |
LOC_Os07g47470.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.520; most accessible tissue: Zhenshan97 flag leaf, score: 99.312 |
| vg0728374936 (J) | chr07 | 28374936 | C | A | 99.80% | 0.00% | C -> T,A | NA |
LOC_Os07g47470.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os07g47470.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 98.920; most accessible tissue: Zhenshan97 flower, score: 99.264 |
| vg0728374999 (J) | chr07 | 28374999 | C | G | 99.00% | 0.00% | C -> G | NA |
LOC_Os07g47470.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 99.303; most accessible tissue: Zhenshan97 flower, score: 99.628 |
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