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Detailed information for vg0402131778:

Variant ID: vg0402131778 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2131778
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.07, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

GATTATGGAAGTGCATGACCATGCCAAAGGTGATTGAGGAGTCTATCACAAGTTATATAATCTATCACAGATTCGAGTGAATGATAGAGCTAATAGAGGA[T/C]
GGCACATATCTAGCCTTGATTTTAATCGTTATCGTGAGGCAAAGGGGTTCATACATGTATACACTAGAGGTTCAGCCGATATAATCTTTATGTATGCCCG

Reverse complement sequence

CGGGCATACATAAAGATTATATCGGCTGAACCTCTAGTGTATACATGTATGAACCCCTTTGCCTCACGATAACGATTAAAATCAAGGCTAGATATGTGCC[A/G]
TCCTCTATTAGCTCTATCATTCACTCGAATCTGTGATAGATTATATAACTTGTGATAGACTCCTCAATCACCTTTGGCATGGTCATGCACTTCCATAATC

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	24.80%	17.60%	0.63%	56.96%	NA
All Indica	2759	14.00%	20.00%	0.94%	65.06%	NA
All Japonica	1512	48.60%	16.30%	0.20%	34.92%	NA
Aus	269	9.30%	0.70%	0.37%	89.59%	NA
Indica I	595	37.10%	3.70%	1.68%	57.48%	NA
Indica II	465	13.80%	5.40%	1.51%	79.35%	NA
Indica III	913	0.70%	38.60%	0.22%	60.57%	NA
Indica Intermediate	786	12.00%	19.60%	0.89%	67.56%	NA
Temperate Japonica	767	75.40%	19.00%	0.26%	5.35%	NA
Tropical Japonica	504	16.50%	15.30%	0.00%	68.25%	NA
Japonica Intermediate	241	30.70%	9.50%	0.41%	59.34%	NA
VI/Aromatic	96	2.10%	10.40%	0.00%	87.50%	NA
Intermediate	90	27.80%	23.30%	0.00%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402131778	T -> C	LOC_Os04g04480.1	intron_variant ; MODIFIER	silent_mutation	Average:10.191; most accessible tissue: Callus, score: 31.636	N	N	N	N
vg0402131778	T -> DEL	N	N	silent_mutation	Average:10.191; most accessible tissue: Callus, score: 31.636	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402131778	NA	2.51E-06	mr1111	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
vg0402131778	NA	6.06E-08	mr1112	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
vg0402131778	NA	1.56E-07	mr1213	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
vg0402131778	2.62E-06	1.82E-06	mr1777	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