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Detailed information for vg1002234112:

Variant ID: vg1002234112 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2234112
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.53, C: 0.47, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

AAGCTCCAGACGAGTATCTGGCCAACGTGGGAACGTGTTTAATGACTAATCAAATCAATGTGCTTAGCGGCGGCTGGTCCGGTGCTAGTCTTCTCCCGGA[T/C]
CTATGTGTTGGCGCTGTCAGTGTGTGGGTGGTGTTTTCCTTTTTTCTGGTTACGACCTTTCAGGGTTGCAATCTTGTAAATTTTTCCTGCTCTATCAATG

Reverse complement sequence

CATTGATAGAGCAGGAAAAATTTACAAGATTGCAACCCTGAAAGGTCGTAACCAGAAAAAAGGAAAACACCACCCACACACTGACAGCGCCAACACATAG[A/G]
TCCGGGAGAAGACTAGCACCGGACCAGCCGCCGCTAAGCACATTGATTTGATTAGTCATTAAACACGTTCCCACGTTGGCCAGATACTCGTCTGGAGCTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.90%	8.90%	0.57%	60.56%	NA
All Indica	2759	14.70%	2.00%	0.47%	82.86%	NA
All Japonica	1512	61.40%	22.50%	0.40%	15.67%	NA
Aus	269	13.00%	0.70%	1.49%	84.76%	NA
Indica I	595	27.40%	5.90%	0.50%	66.22%	NA
Indica II	465	2.80%	0.60%	0.86%	95.70%	NA
Indica III	913	17.40%	0.20%	0.22%	82.15%	NA
Indica Intermediate	786	9.00%	1.80%	0.51%	88.68%	NA
Temperate Japonica	767	51.10%	39.50%	0.13%	9.26%	NA
Tropical Japonica	504	75.60%	2.60%	0.79%	21.03%	NA
Japonica Intermediate	241	64.70%	10.00%	0.41%	24.90%	NA
VI/Aromatic	96	13.50%	21.90%	2.08%	62.50%	NA
Intermediate	90	35.60%	5.60%	2.22%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002234112	T -> C	LOC_Os10g04674.1	upstream_gene_variant ; 2711.0bp to feature; MODIFIER	silent_mutation	Average:8.369; most accessible tissue: Callus, score: 44.413	N	N	N	N
vg1002234112	T -> C	LOC_Os10g04674.3	upstream_gene_variant ; 2711.0bp to feature; MODIFIER	silent_mutation	Average:8.369; most accessible tissue: Callus, score: 44.413	N	N	N	N
vg1002234112	T -> C	LOC_Os10g04674.2	intron_variant ; MODIFIER	silent_mutation	Average:8.369; most accessible tissue: Callus, score: 44.413	N	N	N	N
vg1002234112	T -> DEL	N	N	silent_mutation	Average:8.369; most accessible tissue: Callus, score: 44.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002234112	5.72E-09	5.69E-09	mr1736	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
vg1002234112	1.52E-06	1.52E-06	mr1736	Ind_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