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Detailed information for vg0328876399:

Variant ID: vg0328876399 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 28876399
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTCTCAGTCAGAGGAACCGTTGACAATTGTATCACCAGCGCAGCATCCTTCAAGTTGTACAAACCAAGAGGACTTCAGACCGCTGTTTCATGACAAAT[A/G]
TGATGACAATAGTGGTGGACCGTCCATAGCAACTATTTCAGTAAATGGAGGGTTCAACAGAGTATGTACCTTAGGATTCAAGAGCCAGTGTGAGTTTATG

Reverse complement sequence

CATAAACTCACACTGGCTCTTGAATCCTAAGGTACATACTCTGTTGAACCCTCCATTTACTGAAATAGTTGCTATGGACGGTCCACCACTATTGTCATCA[T/C]
ATTTGTCATGAAACAGCGGTCTGAAGTCCTCTTGGTTTGTACAACTTGAAGGATGCTGCGCTGGTGATACAATTGTCAACGGTTCCTCTGACTGAGACAA

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	76.00%	23.60%	0.02%	0.36%	NA
All Indica	2759	69.80%	29.60%	0.00%	0.62%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	1.50%	98.50%	0.00%	0.00%	NA
Indica I	595	94.80%	5.20%	0.00%	0.00%	NA
Indica II	465	41.10%	57.00%	0.00%	1.94%	NA
Indica III	913	68.70%	31.10%	0.00%	0.22%	NA
Indica Intermediate	786	69.10%	30.20%	0.00%	0.76%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	76.70%	22.20%	1.11%	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
vg0328876399	A -> DEL	LOC_Os03g50570.1	N	frameshift_variant	Average:62.732; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0328876399	A -> G	LOC_Os03g50570.1	missense_variant ; p.Tyr103Cys; MODERATE	nonsynonymous_codon ; Y103C	Average:62.732; most accessible tissue: Zhenshan97 panicle, score: 75.67	benign	0.507	TOLERATED	0.19

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0328876399	NA	2.57E-06	mr1003	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
vg0328876399	NA	3.87E-07	mr1051	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
vg0328876399	NA	5.98E-06	mr1163	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
vg0328876399	NA	3.22E-06	mr1192	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
vg0328876399	NA	1.18E-12	mr1193	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
vg0328876399	NA	2.37E-07	mr1193	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
vg0328876399	NA	4.11E-10	mr1232	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
vg0328876399	NA	7.06E-06	mr1252	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
vg0328876399	NA	1.24E-17	mr1557	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
vg0328876399	NA	3.83E-07	mr1587	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
vg0328876399	7.40E-06	7.39E-06	mr1832	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
vg0328876399	NA	1.03E-07	mr1931	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
vg0328876399	NA	1.28E-06	mr1974	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
vg0328876399	NA	9.96E-06	mr1984	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
vg0328876399	NA	9.70E-12	mr1193_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
vg0328876399	NA	1.66E-16	mr1557_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
vg0328876399	NA	3.62E-07	mr1952_2	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
vg0328876399	6.05E-06	3.20E-08	mr1952_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