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Detailed information for vg0907980770:

Variant ID: vg0907980770 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7980770
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TTACGGTGTAACTTACAGCTGGTAATTTGTACAGTGTAACAACGATTTACTGTTTTTTAAAACGTGATGTAATAAATATAGCTGAAAAAAGAATACATCA[C/T]
GTTAATAGCTAGTTGTATGTATTATTTATGCATAATTTGGAGGCAAATTAAAAGTTCCACTGGTGGAGAAACCCTTTGTAGTCCCGGTTCGTAACCCCCC

Reverse complement sequence

GGGGGGTTACGAACCGGGACTACAAAGGGTTTCTCCACCAGTGGAACTTTTAATTTGCCTCCAAATTATGCATAAATAATACATACAACTAGCTATTAAC[G/A]
TGATGTATTCTTTTTTCAGCTATATTTATTACATCACGTTTTAAAAAACAGTAAATCGTTGTTACACTGTACAAATTACCAGCTGTAAGTTACACCGTAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.10%	35.80%	0.13%	0.00%	NA
All Indica	2759	66.30%	33.50%	0.18%	0.00%	NA
All Japonica	1512	51.70%	48.30%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	82.90%	17.00%	0.17%	0.00%	NA
Indica II	465	24.50%	75.50%	0.00%	0.00%	NA
Indica III	913	84.30%	15.30%	0.33%	0.00%	NA
Indica Intermediate	786	57.50%	42.40%	0.13%	0.00%	NA
Temperate Japonica	767	37.30%	62.60%	0.13%	0.00%	NA
Tropical Japonica	504	78.60%	21.40%	0.00%	0.00%	NA
Japonica Intermediate	241	41.10%	58.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	0.00%	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
vg0907980770	C -> T	LOC_Os09g13660.1	downstream_gene_variant ; 610.0bp to feature; MODIFIER	silent_mutation	Average:28.866; most accessible tissue: Zhenshan97 flower, score: 63.813	N	N	N	N
vg0907980770	C -> T	LOC_Os09g13650-LOC_Os09g13660	intergenic_region ; MODIFIER	silent_mutation	Average:28.866; most accessible tissue: Zhenshan97 flower, score: 63.813	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907980770	NA	1.51E-07	mr1002	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
vg0907980770	NA	2.21E-10	mr1002	Jap_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
vg0907980770	NA	6.87E-06	mr1559	Jap_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
vg0907980770	NA	9.36E-09	mr1942	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
vg0907980770	NA	8.70E-11	mr1002_2	Jap_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
vg0907980770	NA	2.35E-06	mr1011_2	Jap_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
vg0907980770	NA	2.22E-06	mr1201_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
vg0907980770	NA	2.69E-06	mr1295_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
vg0907980770	NA	1.38E-08	mr1330_2	Jap_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
vg0907980770	NA	1.10E-08	mr1379_2	Jap_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
vg0907980770	NA	9.56E-06	mr1409_2	Jap_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
vg0907980770	NA	4.67E-06	mr1438_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
vg0907980770	9.21E-07	9.20E-07	mr1548_2	Jap_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
vg0907980770	NA	1.95E-07	mr1559_2	Jap_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
vg0907980770	NA	8.06E-08	mr1709_2	Jap_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
vg0907980770	NA	9.25E-09	mr1805_2	Jap_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
vg0907980770	NA	4.31E-06	mr1815_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
vg0907980770	NA	1.36E-06	mr1910_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