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Detailed information for vg1002299754:

Variant ID: vg1002299754 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2299754
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.06, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCTTCAGCTCATACGTCTTCTGCAGCACCCACTTGGCAACACCTCCAGAACAGACTTTCCTCTCCCACATTTGAAGGCTGCTGCGAGACAAAGTGGCG[G/A]
CGCCAAGACAATCACCTTCTGTCAGCCAGGTCTGACTGTATGGCTCGGAATCGTAGGGCCATTCAATCACGCTGAGGGTTTGCTTATCCAAATCAAACTG

Reverse complement sequence

CAGTTTGATTTGGATAAGCAAACCCTCAGCGTGATTGAATGGCCCTACGATTCCGAGCCATACAGTCAGACCTGGCTGACAGAAGGTGATTGTCTTGGCG[C/T]
CGCCACTTTGTCTCGCAGCAGCCTTCAAATGTGGGAGAGGAAAGTCTGTTCTGGAGGTGTTGCCAAGTGGGTGCTGCAGAAGACGTATGAGCTGAAGAAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.80%	34.70%	0.21%	0.30%	NA
All Indica	2759	59.70%	39.50%	0.33%	0.47%	NA
All Japonica	1512	84.70%	15.30%	0.00%	0.00%	NA
Aus	269	14.50%	85.50%	0.00%	0.00%	NA
Indica I	595	69.70%	29.70%	0.17%	0.34%	NA
Indica II	465	65.60%	32.90%	0.43%	1.08%	NA
Indica III	913	51.50%	48.20%	0.22%	0.11%	NA
Indica Intermediate	786	58.10%	40.70%	0.51%	0.64%	NA
Temperate Japonica	767	91.50%	8.50%	0.00%	0.00%	NA
Tropical Japonica	504	78.00%	22.00%	0.00%	0.00%	NA
Japonica Intermediate	241	76.80%	23.20%	0.00%	0.00%	NA
VI/Aromatic	96	45.80%	54.20%	0.00%	0.00%	NA
Intermediate	90	60.00%	37.80%	1.11%	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
vg1002299754	G -> A	LOC_Os10g04780.1	missense_variant ; p.Ala273Val; MODERATE	nonsynonymous_codon ; A273V	Average:78.54; most accessible tissue: Minghui63 flag leaf, score: 84.791	unknown	unknown	TOLERATED	0.27
vg1002299754	G -> DEL	LOC_Os10g04780.1	N	frameshift_variant	Average:78.54; most accessible tissue: Minghui63 flag leaf, score: 84.791	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002299754	NA	7.56E-06	mr1179	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
vg1002299754	8.90E-08	NA	mr1486	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
vg1002299754	NA	4.96E-09	mr1486	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
vg1002299754	NA	1.51E-08	mr1510	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
vg1002299754	2.16E-07	NA	mr1548	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
vg1002299754	NA	1.69E-07	mr1548	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
vg1002299754	NA	7.82E-08	mr1588	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
vg1002299754	NA	4.64E-11	mr1624	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
vg1002299754	NA	3.95E-08	mr1624	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
vg1002299754	7.78E-06	NA	mr1751	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
vg1002299754	3.45E-06	NA	mr1486_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
vg1002299754	NA	1.18E-07	mr1486_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
vg1002299754	NA	7.93E-07	mr1721_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