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Detailed information for vg0710831430:

Variant ID: vg0710831430 (JBrowse)	Variation Type: INDEL
Chromosome: chr07	Position: 10831430
Reference Allele: C	Alternative Allele: A,CT,T
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTTTGCAGATTCCCGGCAGCTCGGTAGGAATTTTGATGTGGGACCAAAACCATCTGAAGGTAGACTCCATAAGCTTTCCAACAAGTACTCATGGGTCC[C/A,CT,T]
GAAATTCCTTCTAGATCAGCGGCTAGGTCCATTTGAAGTTGATGCTATCAGGAGGCCCGAATTCGAATCCAAAATATGTAGAACTTTATCTCTTGTCTTC

Reverse complement sequence

GAAGACAAGAGATAAAGTTCTACATATTTTGGATTCGAATTCGGGCCTCCTGATAGCATCAACTTCAAATGGACCTAGCCGCTGATCTAGAAGGAATTTC[G/T,AG,A]
GGACCCATGAGTACTTGTTGGAAAGCTTATGGAGTCTACCTTCAGATGGTTTTGGTCCCACATCAAAATTCCTACCGAGCTGCCGGGAATCTGCAAAACA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.00%	31.90%	2.94%	5.76%	CT: 0.34%; T: 0.02%
All Indica	2759	94.00%	2.80%	1.34%	1.78%	CT: 0.07%
All Japonica	1512	1.40%	80.50%	3.64%	13.96%	CT: 0.53%
Aus	269	41.60%	55.80%	1.49%	0.74%	T: 0.37%
Indica I	595	98.70%	0.70%	0.17%	0.34%	CT: 0.17%
Indica II	465	95.10%	3.70%	0.22%	1.08%	NA
Indica III	913	95.00%	2.20%	1.20%	1.64%	NA
Indica Intermediate	786	88.70%	4.70%	3.05%	3.44%	CT: 0.13%
Temperate Japonica	767	2.00%	69.40%	5.22%	23.34%	CT: 0.13%
Tropical Japonica	504	0.60%	95.80%	0.20%	3.37%	NA
Japonica Intermediate	241	1.20%	83.80%	5.81%	6.22%	CT: 2.90%
VI/Aromatic	96	19.80%	22.90%	40.62%	10.42%	CT: 6.25%
Intermediate	90	48.90%	46.70%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710831430	C -> DEL	N	N	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> CT	LOC_Os07g18270.1	upstream_gene_variant ; 1833.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> CT	LOC_Os07g18260.1	downstream_gene_variant ; 4429.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> CT	LOC_Os07g18280.1	downstream_gene_variant ; 3413.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> CT	LOC_Os07g18270-LOC_Os07g18280	intergenic_region ; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> A	LOC_Os07g18270.1	upstream_gene_variant ; 1832.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> A	LOC_Os07g18260.1	downstream_gene_variant ; 4428.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> A	LOC_Os07g18280.1	downstream_gene_variant ; 3414.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> A	LOC_Os07g18270-LOC_Os07g18280	intergenic_region ; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> T	LOC_Os07g18270.1	upstream_gene_variant ; 1832.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> T	LOC_Os07g18260.1	downstream_gene_variant ; 4428.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> T	LOC_Os07g18280.1	downstream_gene_variant ; 3414.0bp to feature; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N
vg0710831430	C -> T	LOC_Os07g18270-LOC_Os07g18280	intergenic_region ; MODIFIER	silent_mutation	Average:31.303; most accessible tissue: Zhenshan97 flag leaf, score: 45.537	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710831430	1.01E-06	3.87E-07	mr1100	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0710831430	NA	1.49E-09	mr1379	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0710831430	NA	5.86E-08	mr1559	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0710831430	NA	2.34E-09	mr1578	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0710831430	6.18E-07	6.18E-07	mr1598	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0710831430	NA	9.01E-06	mr1619	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0710831430	3.89E-07	3.89E-07	mr1795	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251