323 variations found. Os02g0266100/LOC_Os02g16640 (proline-rich protein HaeIII subfamily 1 precursor; putative; expressed), ranging from 9,506,231 bp to 9,509,762 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g16640 | proline-rich protein HaeIII subfamily 1 precursor, putative, expressed; RAP ID: Os02g0266100; MSU ID: LOC_Os02g16640 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0209508601 (J) | chr02 | 9508601 | TT | TTT | 74.90% | 0.00% | TT -> TTT | NA |
|
| vg0209506303 (J) | chr02 | 9506303 | C | A | 65.60% | 0.00% | A -> C | NA |
LOC_Os02g16640.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.187; most accessible tissue: Minghui63 panicle, score: 96.467 |
| vg0209506313 (J) | chr02 | 9506313 | T | G | 81.30% | 0.40% | T -> G |
LOC_Os02g16640.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g16640.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 92.222; most accessible tissue: Zhenshan97 panicle, score: 96.335 |
|
| vg0209506319 (J) | chr02 | 9506319 | A | C | 96.60% | 0.00% | A -> C | NA |
LOC_Os02g16640.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.249; most accessible tissue: Zhenshan97 panicle, score: 96.375 |
| vg0209506426 (J) | chr02 | 9506426 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g16640.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os02g16650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g16630.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g16630.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.241; most accessible tissue: Zhenshan97 panicle, score: 96.599 |
| vg0209506482 (J) | chr02 | 9506482 | G | GAACC | 85.00% | 0.00% | G -> GAACC | NA |
LOC_Os02g16640.1 Alt: GAACC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 91.226; most accessible tissue: Minghui63 panicle, score: 95.701 |
| vg0209506484 (J) | chr02 | 9506484 | G | GGTTGCA TGGAA | 81.50% | 0.34% | G -> GGTTGCATGG AA,A |
LOC_Os02g16640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g16640.1 Alt: GGTTGCATGGAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os02g16640.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 91.187; most accessible tissue: Minghui63 panicle, score: 95.701 |
|
| vg0209506490 (J) | chr02 | 9506490 | C | T | 81.50% | 0.40% | C -> T |
LOC_Os02g16640.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g16640.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 91.068; most accessible tissue: Minghui63 panicle, score: 95.701 |
|
| vg0209506491 (J) | chr02 | 9506491 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os02g16640.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g16650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g16630.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g16630.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.065; most accessible tissue: Minghui63 panicle, score: 95.701 |
| vg0209506516 (J) | chr02 | 9506516 | T | C | 81.50% | 7.72% | T -> C |
LOC_Os02g16640.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g16640.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 90.519; most accessible tissue: Minghui63 panicle, score: 95.588 |
|
| vg0209506527 (J) | chr02 | 9506527 | GTTGGAA CAT | G | 82.00% | 7.89% | GTTGGAACAT -> G | NA |
LOC_Os02g16640.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g16640.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.329; most accessible tissue: Minghui63 panicle, score: 95.282 |
| vg0209506558 (J) | chr02 | 9506558 | A | T | 82.00% | 7.93% | A -> T |
LOC_Os02g16640.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g16650.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 89.642; most accessible tissue: Zhenshan97 panicle, score: 95.381 |
|
| vg0209506564 (J) | chr02 | 9506564 | G | A | 82.00% | 7.60% | G -> A |
LOC_Os02g16650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 89.589; most accessible tissue: Zhenshan97 panicle, score: 95.381 |
|
| vg0209506565 (J) | chr02 | 9506565 | T | TAC | 81.80% | 8.63% | T -> TAC | NA |
LOC_Os02g16650.1 Alt: TAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: TAC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: TAC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: TAC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 89.589; most accessible tissue: Zhenshan97 panicle, score: 95.381 |
| vg0209506587 (J) | chr02 | 9506587 | T | C | 81.90% | 5.84% | T -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g16650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.413; most accessible tissue: Zhenshan97 panicle, score: 94.440 |
|
| vg0209506594 (J) | chr02 | 9506594 | G | A | 81.90% | 5.14% | G -> A |
LOC_Os02g16650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.320; most accessible tissue: Zhenshan97 panicle, score: 94.440 |
|
| vg0209506595 (J) | chr02 | 9506595 | T | A | 72.20% | 0.00% | T -> A |
mr1084 (All); LR P-value: 1.68E-12;
mr1164 (All); LR P-value: 3.45E-15; mr1164 (Jap_All); LR P-value: 9.63E-06; mr1205 (All); LR P-value: 6.09E-15; mr1281 (All); LR P-value: 2.61E-11; mr1302 (All); LR P-value: 5.69E-10; mr1315 (All); LR P-value: 8.59E-07; mr1332 (All); LR P-value: 2.59E-10; mr1392 (All); LR P-value: 2.21E-06; mr1418 (All); LR P-value: 8.95E-07; mr1420 (All); LR P-value: 2.47E-07; mr1488 (All); LR P-value: 8.35E-10; mr1506 (All); LR P-value: 1.62E-08; mr1508 (All); LR P-value: 4.90E-06; mr1521 (All); LR P-value: 5.08E-14; mr1580 (All); LR P-value: 6.62E-20; mr1604 (All); LR P-value: 2.47E-08; mr1627 (All); LR P-value: 4.30E-23; mr1627 (Jap_All); LR P-value: 5.35E-07; mr1763 (Jap_All); LR P-value: 6.77E-06; mr1764 (All); LR P-value: 5.72E-07; mr1775 (All); LR P-value: 8.30E-13; mr1779 (All); LR P-value: 8.73E-10; mr1797 (All); LR P-value: 6.86E-07; mr1801 (All); LR P-value: 6.86E-07; mr1810 (All); LR P-value: 1.32E-08; mr1824 (All); LR P-value: 2.43E-07; mr1825 (All); LR P-value: 1.16E-16; mr1832 (All); LR P-value: 6.14E-06; mr1886 (All); LR P-value: 1.07E-06; mr1921 (All); LR P-value: 2.56E-10; mr1010_2 (Jap_All); LR P-value: 7.71E-10; mr1084_2 (All); LR P-value: 5.30E-08; mr1164_2 (Jap_All); LR P-value: 8.42E-06; mr1281_2 (All); LR P-value: 3.77E-18; mr1379_2 (All); LR P-value: 7.21E-10; mr1627_2 (All); LR P-value: 3.13E-21; mr1627_2 (Jap_All); LR P-value: 1.31E-06; mr1691_2 (All); LR P-value: 5.52E-07 |
LOC_Os02g16650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.289; most accessible tissue: Zhenshan97 panicle, score: 94.440 |
| vg0209506608 (J) | chr02 | 9506608 | T | G | 81.80% | 0.00% | T -> G |
LOC_Os02g16650.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.793; most accessible tissue: Zhenshan97 panicle, score: 94.278 |
|
| vg0209506609 (J) | chr02 | 9506609 | C | A | 81.80% | 0.00% | C -> A |
LOC_Os02g16650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.724; most accessible tissue: Zhenshan97 panicle, score: 94.278 |
|
| vg0209506629 (J) | chr02 | 9506629 | G | A | 81.70% | 0.00% | G -> A |
LOC_Os02g16650.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.109; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
|
| vg0209506636 (J) | chr02 | 9506636 | G | GTTC | 81.90% | 0.00% | G -> GTTC | NA |
LOC_Os02g16650.1 Alt: GTTC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: GTTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: GTTC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: GTTC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.658; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0209506637 (J) | chr02 | 9506637 | A | AGC | 82.00% | 0.00% | A -> AGC | NA |
LOC_Os02g16650.1 Alt: AGC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: AGC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: AGC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: AGC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.658; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0209506641 (J) | chr02 | 9506641 | T | C | 83.40% | 0.00% | T -> C | NA |
LOC_Os02g16650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.686; most accessible tissue: Zhenshan97 panicle, score: 92.784 |
| vg0209506642 (J) | chr02 | 9506642 | CAGT | C | 84.40% | 0.00% | CAGT -> C | NA |
LOC_Os02g16650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.679; most accessible tissue: Zhenshan97 panicle, score: 92.784 |
| vg0209506647 (J) | chr02 | 9506647 | CATGAT | C | 84.20% | 0.00% | CATGAT -> C | NA |
LOC_Os02g16650.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g16630.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16630.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g16640.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.440; most accessible tissue: Zhenshan97 panicle, score: 92.660 |
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