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Detailed information for vg0721729151:

Variant ID: vg0721729151 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 21729151
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.34, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTAGATGATAACCCTTTTGCTTATGAAGACAAATGTCCACGCAAGGCAGCTAGGTTCGTCGCAGCCAGCCAGTTTATCTGTTACAGTACAGCATAGCA[G/A]
GATCAAAACTTGTCAGGTACATCAAGGATCAGTAATAGCCAACAGAGCTCTTCTTTTACTTCAGGTCTGAGCAAGAAGGCGCCGCACACATCAGCTCACT

Reverse complement sequence

AGTGAGCTGATGTGTGCGGCGCCTTCTTGCTCAGACCTGAAGTAAAAGAAGAGCTCTGTTGGCTATTACTGATCCTTGATGTACCTGACAAGTTTTGATC[C/T]
TGCTATGCTGTACTGTAACAGATAAACTGGCTGGCTGCGACGAACCTAGCTGCCTTGCGTGGACATTTGTCTTCATAAGCAAAAGGGTTATCATCTACTA

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	59.10%	40.80%	0.17%	0.00%	NA
All Indica	2759	92.40%	7.40%	0.22%	0.00%	NA
All Japonica	1512	0.30%	99.70%	0.00%	0.00%	NA
Aus	269	77.30%	22.70%	0.00%	0.00%	NA
Indica I	595	99.00%	0.70%	0.34%	0.00%	NA
Indica II	465	91.80%	8.00%	0.22%	0.00%	NA
Indica III	913	89.30%	10.60%	0.11%	0.00%	NA
Indica Intermediate	786	91.20%	8.50%	0.25%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	0.00%	100.00%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	34.40%	63.30%	2.22%	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
vg0721729151	G -> A	LOC_Os07g36330.1	upstream_gene_variant ; 2753.0bp to feature; MODIFIER	silent_mutation	Average:60.103; most accessible tissue: Zhenshan97 young leaf, score: 80.589	N	N	N	N
vg0721729151	G -> A	LOC_Os07g36340.1	intron_variant ; MODIFIER	silent_mutation	Average:60.103; most accessible tissue: Zhenshan97 young leaf, score: 80.589	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0721729151	NA	9.97E-29	mr1075	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
vg0721729151	NA	3.63E-30	mr1226	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
vg0721729151	NA	5.78E-09	mr1595	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
vg0721729151	NA	1.44E-11	mr1949	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
vg0721729151	NA	6.85E-28	mr1074_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
vg0721729151	NA	4.81E-35	mr1081_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
vg0721729151	NA	5.30E-15	mr1118_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
vg0721729151	NA	2.44E-16	mr1148_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
vg0721729151	NA	1.52E-24	mr1233_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
vg0721729151	NA	2.13E-36	mr1256_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
vg0721729151	NA	1.34E-23	mr1386_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
vg0721729151	NA	2.72E-24	mr1495_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
vg0721729151	NA	2.00E-08	mr1660_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
vg0721729151	NA	1.50E-40	mr1944_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