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Detailed information for vg0143089279:

Variant ID: vg0143089279 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 43089279
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GAAATGTGAACATACGCGTTCCAAGGAATGTGACGGGGGTCGACACGCAACCACTCGCGCGACGTGCGTGGACGGAAGGTGCCGAGCTGTGCACCCTCGA[C/T]
TGATGACAGGAACGAGCAGTGGCTCCTGTCAATCCCACGGTTGAACAGCGCCGGTGTGTCGTACGCCATACCTACATCCAATAGATCGATCAGAAACATA

Reverse complement sequence

TATGTTTCTGATCGATCTATTGGATGTAGGTATGGCGTACGACACACCGGCGCTGTTCAACCGTGGGATTGACAGGAGCCACTGCTCGTTCCTGTCATCA[G/A]
TCGAGGGTGCACAGCTCGGCACCTTCCGTCCACGCACGTCGCGCGAGTGGTTGCGTGTCGACCCCCGTCACATTCCTTGGAACGCGTATGTTCACATTTC

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	66.40%	33.60%	0.08%	0.00%	NA
All Indica	2759	55.10%	44.90%	0.00%	0.00%	NA
All Japonica	1512	91.50%	8.40%	0.07%	0.00%	NA
Aus	269	52.80%	46.50%	0.74%	0.00%	NA
Indica I	595	50.60%	49.40%	0.00%	0.00%	NA
Indica II	465	78.70%	21.30%	0.00%	0.00%	NA
Indica III	913	41.90%	58.10%	0.00%	0.00%	NA
Indica Intermediate	786	59.70%	40.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	77.20%	22.60%	0.20%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	27.10%	71.90%	1.04%	0.00%	NA
Intermediate	90	72.20%	27.80%	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
vg0143089279	C -> T	LOC_Os01g74390.1	missense_variant ; p.Val69Ile; MODERATE	nonsynonymous_codon ; V69I	Average:54.958; most accessible tissue: Minghui63 panicle, score: 73.225	unknown	unknown	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0143089279	NA	2.43E-06	mr1974	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
vg0143089279	3.56E-06	NA	mr1974_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
vg0143089279	1.07E-06	5.38E-09	mr1974_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