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Detailed information for vg0907127691:

Variant ID: vg0907127691 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7127691
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGTGTTGTCGTAATCTTCATCAAAGCCATCCCTGAATAGAACTGGAGCATTATCCAGAGTCTGAATTTCTTCATTCTCAACGGATGATGGCTCAGGAA[C/T]
TGCTTCATCAGTCAAATCAGTCGAAGTGGAAGGTTCAGGTTGCGATTCAACTATTGATGGTTCCTCTATCTTAGACGCCAATGCCTCTGGAGGGGTTTTA

Reverse complement sequence

TAAAACCCCTCCAGAGGCATTGGCGTCTAAGATAGAGGAACCATCAATAGTTGAATCGCAACCTGAACCTTCCACTTCGACTGATTTGACTGATGAAGCA[G/A]
TTCCTGAGCCATCATCCGTTGAGAATGAAGAAATTCAGACTCTGGATAATGCTCCAGTTCTATTCAGGGATGGCTTTGATGAAGATTACGACAACACCCT

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	74.40%	15.60%	0.68%	9.35%	NA
All Indica	2759	70.50%	18.50%	0.98%	10.00%	NA
All Japonica	1512	88.80%	0.50%	0.26%	10.38%	NA
Aus	269	30.90%	68.00%	0.00%	1.12%	NA
Indica I	595	49.10%	49.60%	0.34%	1.01%	NA
Indica II	465	87.10%	10.10%	0.22%	2.58%	NA
Indica III	913	69.30%	3.40%	2.30%	24.97%	NA
Indica Intermediate	786	78.20%	17.60%	0.38%	3.82%	NA
Temperate Japonica	767	98.60%	0.00%	0.13%	1.30%	NA
Tropical Japonica	504	84.90%	0.80%	0.20%	14.09%	NA
Japonica Intermediate	241	66.00%	1.70%	0.83%	31.54%	NA
VI/Aromatic	96	74.00%	25.00%	1.04%	0.00%	NA
Intermediate	90	81.10%	12.20%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907127691	C -> DEL	LOC_Os09g12460.1	N	frameshift_variant	Average:39.323; most accessible tissue: Zhenshan97 young leaf, score: 69.723	N	N	N	N
vg0907127691	C -> T	LOC_Os09g12460.1	missense_variant ; p.Val67Ile; MODERATE	nonsynonymous_codon ; V67I	Average:39.323; most accessible tissue: Zhenshan97 young leaf, score: 69.723	unknown	unknown	TOLERATED	0.26

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907127691	NA	3.96E-08	mr1914	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
vg0907127691	NA	3.66E-06	mr1927	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
vg0907127691	NA	3.99E-06	mr1389_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