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Detailed information for vg0709254491:

Variant ID: vg0709254491 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9254491
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCTCTTAGGTGGAAGGTAACTACTCCCTCCTTCCCTAAATATTTGACACCGTTGACCTTTTGTAACATGTTTGACCGTTCGTTTTATTCAAAAACTTTT[G/A]
TGATATGTGTAAAACTATATGTATACATAAAAGTATATTTAACAATAAATCAAATGATAGAAAAAGAATTAACAATTACTTAAATTTTTTTTGAATAAGA

Reverse complement sequence

TCTTATTCAAAAAAAATTTAAGTAATTGTTAATTCTTTTTCTATCATTTGATTTATTGTTAAATATACTTTTATGTATACATATAGTTTTACACATATCA[C/T]
AAAAGTTTTTGAATAAAACGAACGGTCAAACATGTTACAAAAGGTCAACGGTGTCAAATATTTAGGGAAGGAGGGAGTAGTTACCTTCCACCTAAGAGGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.90%	42.80%	0.19%	0.08%	NA
All Indica	2759	91.30%	8.40%	0.14%	0.11%	NA
All Japonica	1512	5.00%	95.00%	0.00%	0.00%	NA
Aus	269	12.60%	86.20%	1.12%	0.00%	NA
Indica I	595	98.70%	0.80%	0.34%	0.17%	NA
Indica II	465	96.10%	3.70%	0.22%	0.00%	NA
Indica III	913	90.00%	9.70%	0.11%	0.11%	NA
Indica Intermediate	786	84.40%	15.50%	0.00%	0.13%	NA
Temperate Japonica	767	1.60%	98.40%	0.00%	0.00%	NA
Tropical Japonica	504	11.70%	88.30%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	56.70%	40.00%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709254491	G -> DEL	N	N	silent_mutation	Average:47.444; most accessible tissue: Minghui63 young leaf, score: 78.443	N	N	N	N
vg0709254491	G -> A	LOC_Os07g15920.1	downstream_gene_variant ; 4208.0bp to feature; MODIFIER	silent_mutation	Average:47.444; most accessible tissue: Minghui63 young leaf, score: 78.443	N	N	N	N
vg0709254491	G -> A	LOC_Os07g15930.1	intron_variant ; MODIFIER	silent_mutation	Average:47.444; most accessible tissue: Minghui63 young leaf, score: 78.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709254491	NA	2.47E-16	mr1147	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
vg0709254491	NA	1.74E-13	mr1270	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
vg0709254491	NA	3.08E-11	mr1316	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
vg0709254491	NA	6.27E-13	mr1914	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
vg0709254491	NA	3.70E-07	mr1302_2	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
vg0709254491	NA	2.86E-29	mr1580_2	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
vg0709254491	3.10E-06	3.65E-07	mr1713_2	Ind_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
vg0709254491	NA	3.61E-29	mr1825_2	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
vg0709254491	NA	9.97E-06	mr1862_2	Ind_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
vg0709254491	NA	6.30E-17	mr1870_2	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
vg0709254491	NA	2.53E-25	mr1943_2	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