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Detailed information for vg0311297778:

Variant ID: vg0311297778 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 11297778
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

AATCAACAGAGCAGTGCATAATGTTGAGGCCGAACCACATGACCGGGCGAAGCACGCGCTAAAGTCCGCCCCTCACGGCAAGATAATCAAGATGCAGATT[G/A]
ATGACGCCGACCCCACAAAGCTCGTATCGCTGGGGGGCGACATGGGCGAAGAAGAGGCTGCGAACATTCTAGAGGTACTCAAGAAAAATAGTGATATCTT

Reverse complement sequence

AAGATATCACTATTTTTCTTGAGTACCTCTAGAATGTTCGCAGCCTCTTCTTCGCCCATGTCGCCCCCCAGCGATACGAGCTTTGTGGGGTCGGCGTCAT[C/T]
AATCTGCATCTTGATTATCTTGCCGTGAGGGGCGGACTTTAGCGCGTGCTTCGCCCGGTCATGTGGTTCGGCCTCAACATTATGCACTGCTCTGTTGATT

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	87.80%	7.40%	3.07%	1.80%	NA
All Indica	2759	79.90%	11.90%	5.11%	3.08%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	88.20%	5.20%	5.38%	1.18%	NA
Indica II	465	27.10%	46.20%	14.41%	12.26%	NA
Indica III	913	99.30%	0.40%	0.22%	0.00%	NA
Indica Intermediate	786	82.20%	10.10%	5.09%	2.67%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	14.40%	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
vg0311297778	G -> A	LOC_Os03g20050.1	missense_variant ; p.Asp140Asn; MODERATE	nonsynonymous_codon ; D140N	Average:52.797; most accessible tissue: Minghui63 flag leaf, score: 71.116	possibly damaging	1.641	DELETERIOUS	0.03
vg0311297778	G -> DEL	LOC_Os03g20050.1	N	frameshift_variant	Average:52.797; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0311297778	NA	3.78E-06	mr1231	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
vg0311297778	NA	4.72E-06	mr1040_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
vg0311297778	4.81E-06	NA	mr1301_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
vg0311297778	NA	1.21E-07	mr1362_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
vg0311297778	NA	5.34E-06	mr1406_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
vg0311297778	7.16E-06	7.16E-06	mr1424_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
vg0311297778	NA	6.78E-06	mr1482_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
vg0311297778	NA	8.99E-06	mr1611_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
vg0311297778	NA	7.49E-06	mr1787_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
vg0311297778	NA	3.58E-07	mr1830_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
vg0311297778	1.70E-06	NA	mr1846_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
vg0311297778	5.55E-07	NA	mr1846_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
vg0311297778	3.12E-06	2.19E-07	mr1938_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