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Detailed information for vg0702311691:

Variant ID: vg0702311691 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2311691
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCAACGTCGCCTCCAAGGTCCTCGCCAAGGTCATCGAATACTGCATCAAGCACGCCGCCGCCGGGGAGGAGGAGGAGAAGGATCTGAAGAGCTTCGAC[G/A]
CCGAGTTCATCGATGTGGACAAGAACATGCTGTACGACCTGCTCCTGGCGTCCAATTTCATGAACATCAAGAGCTTGCTGGATTTGTGCTGCCAGCACAC

Reverse complement sequence

GTGTGCTGGCAGCACAAATCCAGCAAGCTCTTGATGTTCATGAAATTGGACGCCAGGAGCAGGTCGTACAGCATGTTCTTGTCCACATCGATGAACTCGG[C/T]
GTCGAAGCTCTTCAGATCCTTCTCCTCCTCCTCCCCGGCGGCGGCGTGCTTGATGCAGTATTCGATGACCTTGGCGAGGACCTTGGAGGCGACGTTGGGG

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	50.70%	48.90%	0.11%	0.36%	NA
All Indica	2759	83.80%	15.50%	0.14%	0.54%	NA
All Japonica	1512	0.90%	99.10%	0.00%	0.00%	NA
Aus	269	5.20%	94.80%	0.00%	0.00%	NA
Indica I	595	94.80%	4.90%	0.00%	0.34%	NA
Indica II	465	50.50%	48.60%	0.00%	0.86%	NA
Indica III	913	94.20%	5.40%	0.11%	0.33%	NA
Indica Intermediate	786	83.10%	15.80%	0.38%	0.76%	NA
Temperate Japonica	767	0.00%	100.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	34.40%	62.20%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0702311691	G -> DEL	LOC_Os07g05180.1	N	frameshift_variant	Average:61.645; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0702311691	G -> A	LOC_Os07g05180.1	missense_variant ; p.Ala92Thr; MODERATE	nonsynonymous_codon ; A92T	Average:61.645; most accessible tissue: Zhenshan97 panicle, score: 78.302	benign	1.48	TOLERATED	0.11

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702311691	NA	5.86E-06	mr1216	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
vg0702311691	NA	2.26E-07	mr1836	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
vg0702311691	NA	1.47E-06	mr1158_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
vg0702311691	NA	3.31E-12	mr1158_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
vg0702311691	NA	7.74E-13	mr1383_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
vg0702311691	NA	3.25E-09	mr1478_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
vg0702311691	NA	9.56E-06	mr1648_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
vg0702311691	NA	5.50E-22	mr1971_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