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Detailed information for vg1003053735:

Variant ID: vg1003053735 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3053735
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, C: 0.31, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

CCTACGGAGTCGCTAGATCCTCTTGGCTTAGTGACCGAAGGTTGAGGGGAGTTACTACCCTCAAACTTCCCGGCCTCCCCCTTGATAGCCGGCAAATATA[C/T]
TTCTACTATTATCATATAAAACATCTGCAGCAATGCGTGAGATCCCGTGTAGTTAATTACTCCATCCATTCTTTAATAGATGACGACGTTGATTTTTAGA

Reverse complement sequence

TCTAAAAATCAACGTCGTCATCTATTAAAGAATGGATGGAGTAATTAACTACACGGGATCTCACGCATTGCTGCAGATGTTTTATATGATAATAGTAGAA[G/A]
TATATTTGCCGGCTATCAAGGGGGAGGCCGGGAAGTTTGAGGGTAGTAACTCCCCTCAACCTTCGGTCACTAAGCCAAGAGGATCTAGCGACTCCGTAGG

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	53.70%	45.30%	0.32%	0.66%	NA
All Indica	2759	35.00%	63.40%	0.40%	1.12%	NA
All Japonica	1512	98.80%	1.10%	0.07%	0.00%	NA
Aus	269	3.30%	96.70%	0.00%	0.00%	NA
Indica I	595	34.60%	64.90%	0.50%	0.00%	NA
Indica II	465	31.00%	68.20%	0.65%	0.22%	NA
Indica III	913	29.60%	67.70%	0.22%	2.52%	NA
Indica Intermediate	786	44.10%	54.60%	0.38%	0.89%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	51.10%	45.60%	3.33%	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
vg1003053735	C -> T	LOC_Os10g06020.1	missense_variant ; p.Val19Ile; MODERATE	nonsynonymous_codon ; V19I	Average:49.38; most accessible tissue: Callus, score: 71.302	unknown	unknown	TOLERATED	0.86
vg1003053735	C -> DEL	LOC_Os10g06020.1	N	frameshift_variant	Average:49.38; most accessible tissue: Callus, score: 71.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003053735	NA	9.83E-07	mr1503	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
vg1003053735	NA	3.04E-07	mr1690	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
vg1003053735	8.32E-07	NA	mr1709	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
vg1003053735	1.51E-06	1.09E-10	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
vg1003053735	NA	7.71E-06	mr1574_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
vg1003053735	1.70E-13	5.85E-09	mr1709_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
vg1003053735	1.20E-12	2.99E-18	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