RiceVarMap2

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76 variations found. LOC_Os07g40550 (IBS1; putative; expressed), ranging from 24,292,559 bp to 24,298,863 bp (including 0 kb upstream and 0 kb downstream of the gene).

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

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.

Detailed Variation Information:

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Var ID	Chrom	Position	Primary Allele	Secondary Allele	Primary Allele Frequency	DEL Frequency	Var	GWAS Results	Effect
STR0724294126 (J)	chr07	24294126	TGATCAT GATCA	TGATCAT GATCT	89.90%	0.00%	TGATCATGAT CA -> TGATCATGAT CT	NA
STR0724297406 (J)	chr07	24297406	TT	T	49.10%	0.00%	TT -> T	NA
STR0724297427 (J)	chr07	24297427	T	A	99.20%	0.00%	T -> A	NA
STR0724298615 (J)	chr07	24298615	TCG	TCC	47.30%	0.00%	TCG -> TCC	NA
vg0724292593 (J)	chr07	24292593	C	T	73.20%	0.17%	C -> T	mr1174 (All); LR P-value: 8.44E-09; mr1347 (All); LR P-value: 8.52E-07	N Alt: DEL/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.990; most accessible tissue: Minghui63 root, score: 84.686
vg0724292629 (J)	chr07	24292629	G	A	98.80%	0.00%	G -> A	NA	LOC_Os07g40550.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.203; most accessible tissue: Minghui63 root, score: 82.967
vg0724292641 (J)	chr07	24292641	C	A	56.90%	0.36%	C -> A	mr1125_2 (Ind_All); LR P-value: 6.55E-06; mr1170_2 (All); LR P-value: 2.33E-08	N Alt: DEL/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: A\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.582; most accessible tissue: Minghui63 root, score: 82.667
vg0724292753 (J)	chr07	24292753	C	T	57.10%	0.49%	C -> T	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.346; most accessible tissue: Callus, score: 92.881
vg0724292816 (J)	chr07	24292816	TTTTCTT TGTATC	T	57.30%	0.11%	TTTTCTTTGT ATC -> T	NA	N Alt: DEL/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: T\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.957; most accessible tissue: Callus, score: 92.881
vg0724293057 (J)	chr07	24293057	G	GAA	42.10%	0.04%	GAA -> G,GA	NA	LOC_Os07g40550.1 Alt: GA\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: GA\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: GA\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: GA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: G\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: G\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: G\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 69.171; most accessible tissue: Callus, score: 93.205
vg0724293344 (J)	chr07	24293344	T	C	72.50%	0.19%	T -> C	mr1174 (All); LR P-value: 7.09E-09; mr1347 (All); LR P-value: 1.31E-06	N Alt: DEL/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: C\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: C\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: C\| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.821; most accessible tissue: Minghui63 root, score: 72.958
vg0724293447 (J)	chr07	24293447	T	A	72.80%	0.00%	T -> A	mr1174 (All); LR P-value: 1.93E-08; mr1347 (All); LR P-value: 1.92E-06	LOC_Os07g40540.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.027; most accessible tissue: Callus, score: 81.730
vg0724293529 (J)	chr07	24293529	C	T	99.80%	0.00%	C -> T	NA	LOC_Os07g40540.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g40550.1 Alt: T\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.2 Alt: T\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.3 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 47.845; most accessible tissue: Callus, score: 81.730
vg0724293530 (J)	chr07	24293530	C	A	99.20%	0.00%	C -> A,T	NA	LOC_Os07g40540.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.112; most accessible tissue: Callus, score: 81.730
vg0724293536 (J)	chr07	24293536	C	CATATTA ATGTTA	99.90%	0.00%	C -> A,CATATTAA TGTTA	NA	LOC_Os07g40540.1 Alt: CATATTAATGTTA\| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g40550.1 Alt: CATATTAATGTTA\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.2 Alt: CATATTAATGTTA\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.3 Alt: CATATTAATGTTA\| intron_variant MODIFIER(snpEff) LOC_Os07g40540.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g40550.1 Alt: A\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.2 Alt: A\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.3 Alt: A\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.303; most accessible tissue: Callus, score: 81.730
vg0724293541 (J)	chr07	24293541	T	C	57.80%	0.19%	T -> C	mr1170_2 (All); LR P-value: 4.02E-08; mr1699_2 (Ind_All); LR P-value: 4.63E-06	N Alt: DEL/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: C\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: C\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.900; most accessible tissue: Callus, score: 81.730
vg0724293542 (J)	chr07	24293542	A	G	57.00%	0.23%	A -> G	mr1170_2 (All); LR P-value: 4.60E-08; mr1699_2 (Ind_All); LR P-value: 4.63E-06	N Alt: DEL/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.958; most accessible tissue: Callus, score: 81.730
vg0724293558 (J)	chr07	24293558	GAC	GATAC	99.80%	0.00%	GAC -> GATAC,G	NA	LOC_Os07g40540.1 Alt: GATAC\| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g40550.1 Alt: GATAC\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.2 Alt: GATAC\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.3 Alt: GATAC\| intron_variant MODIFIER(snpEff) LOC_Os07g40540.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g40550.1 Alt: G\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.2 Alt: G\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.3 Alt: G\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 46.223; most accessible tissue: Callus, score: 81.730
vg0724293560 (J)	chr07	24293560	C	G	99.80%	0.00%	C -> G,T	NA	LOC_Os07g40540.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g40550.1 Alt: G\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.2 Alt: G\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.3 Alt: G\| intron_variant MODIFIER(snpEff) LOC_Os07g40540.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g40550.1 Alt: T\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.2 Alt: T\| intron_variant MODIFIER(snpEff) LOC_Os07g40550.3 Alt: T\| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 46.223; most accessible tissue: Callus, score: 81.730
vg0724293602 (J)	chr07	24293602	A	G	98.50%	0.00%	A -> G	NA	LOC_Os07g40540.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.619; most accessible tissue: Minghui63 root, score: 57.225
vg0724293632 (J)	chr07	24293632	C	T	98.20%	0.00%	C -> T	NA	LOC_Os07g40540.1 Alt: T\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: T\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.627; most accessible tissue: Minghui63 root, score: 56.226
vg0724293671 (J)	chr07	24293671	G	A	56.90%	0.15%	G -> A	mr1125_2 (Ind_All); LR P-value: 4.84E-06; mr1170_2 (All); LR P-value: 4.58E-08; mr1699_2 (Ind_All); LR P-value: 2.78E-06	N Alt: DEL/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.113; most accessible tissue: Minghui63 young leaf, score: 61.007
vg0724293857 (J)	chr07	24293857	C	A	98.60%	0.00%	C -> A	NA	LOC_Os07g40540.1 Alt: A\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: A\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.120; most accessible tissue: Minghui63 root, score: 65.279
vg0724293899 (J)	chr07	24293899	GA	GAA	71.00%	0.00%	GA -> GAA,G,GAAA	NA	LOC_Os07g40540.1 Alt: GAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: GAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: GAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: GAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: GAAA\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: GAAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: GAAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: GAAA\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40540.1 Alt: G\| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.1 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.2 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g40550.3 Alt: G\| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.399; most accessible tissue: Minghui63 root, score: 70.332
vg0724294020 (J)	chr07	24294020	T	C	72.40%	0.23%	T -> C	mr1174 (All); LR P-value: 7.86E-09; mr1347 (All); LR P-value: 1.34E-06	LOC_Os07g40550.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g40550.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g40550.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os07g40550.1 Alt: C\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os07g40550.2 Alt: C\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os07g40550.3 Alt: C\| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 53.411; most accessible tissue: Callus, score: 85.698

Showing 1 to 25 of 76 entries

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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
Upstream (kb, optional, must <= 10 kb) :	Downstream (kb, optional, must <= 10 kb) :
Variations Type: All SNP Only INDEL Only STR Only
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Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

Detailed Variation Information:

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