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Detailed information for vg1121947567:

Variant ID: vg1121947567 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21947567
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

AAGACAAATATGGTGCTCAAAGATTTTGGTGGTAATCCATCGGAGACCAAAGGTGTTTTAAATGTGGAGCTGACAGTCGGCAGTAAAACTATTCCTACCA[C/T]
GTTTTTTGTCATTGATGGGAAGGGTTCATACAGTTTGTTGCTTGGAAGATATTGGATTCATGCCAATTGTTGCATCCCTTCAACTATGCATCAGTGCTTG

Reverse complement sequence

CAAGCACTGATGCATAGTTGAAGGGATGCAACAATTGGCATGAATCCAATATCTTCCAAGCAACAAACTGTATGAACCCTTCCCATCAATGACAAAAAAC[G/A]
TGGTAGGAATAGTTTTACTGCCGACTGTCAGCTCCACATTTAAAACACCTTTGGTCTCCGATGGATTACCACCAAAATCTTTGAGCACCATATTTGTCTT

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	82.80%	13.60%	0.95%	2.62%	NA
All Indica	2759	93.80%	3.10%	0.47%	2.57%	NA
All Japonica	1512	70.20%	27.40%	0.73%	1.65%	NA
Aus	269	70.30%	16.70%	5.20%	7.81%	NA
Indica I	595	99.30%	0.30%	0.00%	0.34%	NA
Indica II	465	98.90%	0.60%	0.22%	0.22%	NA
Indica III	913	89.40%	5.50%	0.77%	4.38%	NA
Indica Intermediate	786	91.90%	3.90%	0.64%	3.56%	NA
Temperate Japonica	767	88.40%	11.30%	0.13%	0.13%	NA
Tropical Japonica	504	38.90%	55.80%	1.39%	3.97%	NA
Japonica Intermediate	241	77.60%	19.50%	1.24%	1.66%	NA
VI/Aromatic	96	14.60%	75.00%	6.25%	4.17%	NA
Intermediate	90	67.80%	27.80%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121947567	C -> T	LOC_Os11g37170.1	missense_variant ; p.Thr835Met; MODERATE	nonsynonymous_codon ; T835M	Average:28.984; most accessible tissue: Minghui63 flag leaf, score: 42.036	benign	0.903	DELETERIOUS	0.04
vg1121947567	C -> DEL	LOC_Os11g37170.1	N	frameshift_variant	Average:28.984; most accessible tissue: Minghui63 flag leaf, score: 42.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121947567	NA	5.94E-06	mr1029	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
vg1121947567	NA	6.40E-06	mr1045	Jap_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
vg1121947567	NA	1.84E-10	mr1070	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
vg1121947567	NA	4.09E-06	mr1189	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
vg1121947567	NA	3.73E-08	mr1442	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
vg1121947567	4.22E-06	1.68E-06	mr1470	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
vg1121947567	7.85E-06	7.83E-06	mr1481	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
vg1121947567	NA	9.00E-09	mr1563	Jap_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
vg1121947567	NA	9.55E-06	mr1596	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
vg1121947567	NA	1.50E-06	mr1629	Jap_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
vg1121947567	NA	2.63E-08	mr1671	Jap_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
vg1121947567	1.24E-06	NA	mr1679	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
vg1121947567	NA	2.34E-09	mr1679	Jap_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
vg1121947567	NA	6.89E-06	mr1780	Jap_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
vg1121947567	6.87E-06	NA	mr1982	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
vg1121947567	NA	1.42E-07	mr1982	Jap_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
vg1121947567	NA	1.17E-06	mr1990	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
vg1121947567	5.21E-06	5.21E-06	mr1760_2	Jap_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