34 variations found. Os07g0107900/LOC_Os07g01720 (expressed protein), ranging from 428,797 bp to 431,747 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os07g01720 | expressed protein; RAP ID: Os07g0107900; MSU ID: LOC_Os07g01720 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0700428870 (J) | chr07 | 428870 | C | T | 51.50% | 0.00% | T -> C |
mr1110 (Ind_All); LR P-value: 8.64E-09;
mr1216 (All); LR P-value: 1.18E-06; mr1216 (Ind_All); LR P-value: 2.16E-07; mr1110_2 (Ind_All); LR P-value: 1.14E-06; mr1158_2 (Ind_All); LR P-value: 1.32E-10; mr1383_2 (Ind_All); LR P-value: 2.89E-12; mr1478_2 (All); LR P-value: 2.29E-09; mr1889_2 (Ind_All); LR P-value: 3.49E-09 |
LOC_Os07g01720.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os07g01720.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700428888 (J) | chr07 | 428888 | C | CGCCACA CGGGCAA T | 51.40% | 0.19% | CGCCACACGG GCAAT -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01720.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700428928 (J) | chr07 | 428928 | CGGAGGA | C | 98.20% | 0.00% | CGGAGGA -> C,CGGA | NA |
LOC_Os07g01720.1 Alt: CGGA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: CGGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: CGGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01720.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700428967 (J) | chr07 | 428967 | T | TA | 79.90% | 0.00% | T -> TA | NA |
LOC_Os07g01720.1 Alt: TA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429090 (J) | chr07 | 429090 | GAA | G | 56.70% | 0.17% | G -> GAA | NA |
LOC_Os07g01720.1 Alt: GAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429101 (J) | chr07 | 429101 | AAG | A | 98.00% | 0.00% | AAG -> A | NA |
LOC_Os07g01720.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429133 (J) | chr07 | 429133 | GAA | GA | 49.30% | 0.00% | GA -> GAA,GAAA,G ,TA | NA |
LOC_Os07g01720.1 Alt: GAAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: GAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01720.1 Alt: GAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01730.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01720.1 Alt: TA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01730.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01720.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os07g01730.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429218 (J) | chr07 | 429218 | A | C | 98.70% | 0.00% | A -> C | NA |
LOC_Os07g01720.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429232 (J) | chr07 | 429232 | G | T | 53.40% | 0.30% | T -> G |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01720.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01730.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0700429581 (J) | chr07 | 429581 | G | C | 53.30% | 1.61% | C -> G |
LOC_Os07g01720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g01720.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0700429583 (J) | chr07 | 429583 | A | C | 96.90% | 1.29% | A -> C | NA |
LOC_Os07g01720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g01720.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429585 (J) | chr07 | 429585 | G | A | 51.90% | 1.65% | G -> A |
mr1110 (Ind_All); LR P-value: 4.56E-09;
mr1216 (All); LR P-value: 1.11E-06; mr1216 (Ind_All); LR P-value: 3.91E-06; mr1598 (All); LR P-value: 2.05E-19; mr1990 (All); LR P-value: 3.92E-06; mr1158_2 (All); LR P-value: 4.00E-07; mr1158_2 (Ind_All); LR P-value: 4.15E-10; mr1383_2 (Ind_All); LR P-value: 4.30E-12; mr1478_2 (All); LR P-value: 1.78E-09; mr1655_2 (All); LR P-value: 7.94E-06; mr1728_2 (All); LR P-value: 5.62E-11; mr1889_2 (Ind_All); LR P-value: 4.44E-08 |
LOC_Os07g01720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g01720.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429586 (J) | chr07 | 429586 | TC | T | 98.40% | 0.00% | TC -> T | NA |
LOC_Os07g01720.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429790 (J) | chr07 | 429790 | G | T | 95.20% | 0.00% | G -> T |
LOC_Os07g01720.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
|
| vg0700429822 (J) | chr07 | 429822 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os07g01720.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os07g01730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429828 (J) | chr07 | 429828 | C | T | 96.80% | 0.00% | C -> T | NA |
LOC_Os07g01720.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429884 (J) | chr07 | 429884 | GGAA | G | 96.50% | 0.00% | GGAA -> G,AGAA | NA |
LOC_Os07g01720.1 Alt: AGAA| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os07g01720.1 Alt: G| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700429946 (J) | chr07 | 429946 | A | G | 98.90% | 0.00% | A -> G | NA |
LOC_Os07g01720.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700430066 (J) | chr07 | 430066 | G | A | 98.40% | 0.00% | G -> A | NA |
LOC_Os07g01720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700430085 (J) | chr07 | 430085 | G | A | 99.10% | 0.00% | G -> A | NA |
LOC_Os07g01720.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g01730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700430374 (J) | chr07 | 430374 | G | A | 53.40% | 0.13% | G -> A |
mr1032 (All); LR P-value: 4.12E-14;
mr1110 (Ind_All); LR P-value: 7.89E-09; mr1216 (All); LR P-value: 1.97E-06; mr1216 (Ind_All); LR P-value: 3.92E-06; mr1478 (All); LR P-value: 1.02E-13; mr1796 (All); LR P-value: 1.08E-06; mr1990 (All); LR P-value: 1.92E-06; mr1158_2 (All); LR P-value: 2.19E-06; mr1158_2 (Ind_All); LR P-value: 1.24E-09; mr1268_2 (Ind_All); LR P-value: 3.56E-06; mr1383_2 (Ind_All); LR P-value: 6.62E-11; mr1478_2 (All); LR P-value: 1.45E-09; mr1728_2 (All); LR P-value: 2.92E-11; mr1889_2 (Ind_All); LR P-value: 1.22E-08 |
LOC_Os07g01720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g01720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700430396 (J) | chr07 | 430396 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os07g01720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700430672 (J) | chr07 | 430672 | A | C | 98.40% | 0.00% | A -> C | NA |
LOC_Os07g01720.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700430775 (J) | chr07 | 430775 | G | A | 53.40% | 0.25% | G -> A |
mr1110 (Ind_All); LR P-value: 9.65E-09;
mr1216 (All); LR P-value: 8.56E-07; mr1216 (Ind_All); LR P-value: 8.19E-07; mr1598 (All); LR P-value: 2.35E-19; mr1990 (All); LR P-value: 1.26E-06; mr1110_2 (Ind_All); LR P-value: 1.67E-06; mr1158_2 (All); LR P-value: 7.65E-07; mr1158_2 (Ind_All); LR P-value: 1.25E-10; mr1383_2 (Ind_All); LR P-value: 1.27E-11; mr1478_2 (All); LR P-value: 9.14E-10; mr1479_2 (All); LR P-value: 2.38E-06; mr1655_2 (All); LR P-value: 6.19E-06; mr1728_2 (All); LR P-value: 1.50E-11; mr1889_2 (Ind_All); LR P-value: 5.72E-09 |
LOC_Os07g01720.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g01720.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700430789 (J) | chr07 | 430789 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os07g01720.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g01730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g01710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700430820 (J) | chr07 | 430820 | G | T | 80.00% | 0.00% | G -> T | NA |
LOC_Os07g01720.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700431332 (J) | chr07 | 431332 | T | C | 97.90% | 0.00% | T -> C | NA |
LOC_Os07g01720.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700431475 (J) | chr07 | 431475 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os07g01720.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700431504 (J) | chr07 | 431504 | T | G | 98.40% | 0.00% | T -> G | NA |
LOC_Os07g01720.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700431536 (J) | chr07 | 431536 | A | T | 99.10% | 0.00% | A -> T | NA |
LOC_Os07g01720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700431577 (J) | chr07 | 431577 | A | T | 96.80% | 0.00% | A -> T | NA |
LOC_Os07g01720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700431655 (J) | chr07 | 431655 | T | C | 55.60% | 0.32% | C -> T |
mr1005 (All); LR P-value: 5.16E-10;
mr1110 (Ind_All); LR P-value: 1.50E-08; mr1216 (Ind_All); LR P-value: 4.11E-06; mr1495 (All); LR P-value: 1.20E-25; mr1835 (All); LR P-value: 4.30E-06; mr1904 (All); LR P-value: 4.93E-12; mr1110_2 (Ind_All); LR P-value: 1.37E-06; mr1158_2 (Ind_All); LR P-value: 3.67E-10; mr1383_2 (Ind_All); LR P-value: 3.95E-11; mr1495_2 (All); LR P-value: 1.23E-23; mr1889_2 (Ind_All); LR P-value: 3.09E-08; mr1904_2 (All); LR P-value: 6.06E-13 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g01720.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01730.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0700431681 (J) | chr07 | 431681 | T | C | 95.20% | 0.00% | T -> C | NA |
LOC_Os07g01720.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g01730.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g01710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| STR0700429885 (J) | chr07 | 429885 | GAAGAAG AAGAAG | GAAGAAG AAG | 99.00% | 0.00% | GAAGAAGAAG AAG -> GAAGAAGAAG | NA |
|