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Detailed information for vg1003095982:

Variant ID: vg1003095982 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3095982
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTGTTACGGCTAAAATATAATGAACTTGAATATGAGACTTTATATATATGTGTAGTACTAATAGGAGTAAATGTTTAATTTTATAGAATTTTTCGTGA[T/C]
ATTTGTTAGTTGGTGCGCACGAGAAACATGTGTACATAGAATATGTTCCTGGTAACCATATATGATCTTTAGTGAGTTACAAATATCCTAACTATTTTCA

Reverse complement sequence

TGAAAATAGTTAGGATATTTGTAACTCACTAAAGATCATATATGGTTACCAGGAACATATTCTATGTACACATGTTTCTCGTGCGCACCAACTAACAAAT[A/G]
TCACGAAAAATTCTATAAAATTAAACATTTACTCCTATTAGTACTACACATATATATAAAGTCTCATATTCAAGTTCATTATATTTTAGCCGTAACAAAA

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	59.10%	34.80%	0.32%	5.78%	NA
All Indica	2759	57.60%	41.10%	0.14%	1.12%	NA
All Japonica	1512	72.60%	11.40%	0.53%	15.48%	NA
Aus	269	7.10%	92.90%	0.00%	0.00%	NA
Indica I	595	64.50%	34.80%	0.00%	0.67%	NA
Indica II	465	40.00%	59.40%	0.43%	0.22%	NA
Indica III	913	70.20%	27.40%	0.22%	2.19%	NA
Indica Intermediate	786	48.20%	51.00%	0.00%	0.76%	NA
Temperate Japonica	767	62.20%	10.70%	0.78%	26.34%	NA
Tropical Japonica	504	87.70%	11.50%	0.00%	0.79%	NA
Japonica Intermediate	241	74.30%	13.30%	0.83%	11.62%	NA
VI/Aromatic	96	40.60%	54.20%	0.00%	5.21%	NA
Intermediate	90	51.10%	42.20%	3.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003095982	T -> C	LOC_Os10g06090.1	intron_variant ; MODIFIER	silent_mutation	Average:28.091; most accessible tissue: Callus, score: 50.957	N	N	N	N
vg1003095982	T -> DEL	N	N	silent_mutation	Average:28.091; most accessible tissue: Callus, score: 50.957	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003095982	NA	9.54E-06	mr1210	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
vg1003095982	NA	6.20E-06	mr1305	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
vg1003095982	NA	1.01E-06	mr1547	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
vg1003095982	NA	5.61E-06	mr1547	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
vg1003095982	NA	5.57E-07	mr1585	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
vg1003095982	NA	6.87E-06	mr1586	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
vg1003095982	2.43E-13	1.59E-26	mr1709	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
vg1003095982	2.13E-11	1.58E-21	mr1709	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
vg1003095982	NA	1.68E-06	mr1062_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
vg1003095982	NA	8.51E-08	mr1547_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
vg1003095982	4.60E-27	3.58E-53	mr1709_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
vg1003095982	9.42E-19	4.50E-32	mr1709_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
vg1003095982	4.50E-11	2.23E-19	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
vg1003095982	NA	1.01E-06	mr1743_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