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Detailed information for vg0819104472:

Variant ID: vg0819104472 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19104472
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.02, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTGATTGTAGGATCAAATCAACTGGCACGCTTGCATACCCGAAGGCGAGTTTTGGACCTGCACTGGAGTTAAGCAGATATCCCAGGCCTCGTGTTTTA[T/C]
GTCAACACGCTTTTGGTACGCCTGGTGGGACAGATCAGAAGTCAGAATCACAACAACAGTTTTTCCCATGGCCGAGAAACCGCCAGCATCGCCGTCCTCG

Reverse complement sequence

CGAGGACGGCGATGCTGGCGGTTTCTCGGCCATGGGAAAAACTGTTGTTGTGATTCTGACTTCTGATCTGTCCCACCAGGCGTACCAAAAGCGTGTTGAC[A/G]
TAAAACACGAGGCCTGGGATATCTGCTTAACTCCAGTGCAGGTCCAAAACTCGCCTTCGGGTATGCAAGCGTGCCAGTTGATTTGATCCTACAATCAACA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.30%	9.90%	19.51%	4.32%	NA
All Indica	2759	54.40%	16.20%	26.86%	2.57%	NA
All Japonica	1512	87.90%	0.30%	3.04%	8.80%	NA
Aus	269	52.00%	3.70%	44.24%	0.00%	NA
Indica I	595	51.60%	6.60%	39.16%	2.69%	NA
Indica II	465	35.50%	28.60%	32.90%	3.01%	NA
Indica III	913	63.20%	16.50%	17.74%	2.52%	NA
Indica Intermediate	786	57.40%	15.80%	24.55%	2.29%	NA
Temperate Japonica	767	99.60%	0.00%	0.39%	0.00%	NA
Tropical Japonica	504	67.90%	0.60%	8.33%	23.21%	NA
Japonica Intermediate	241	92.50%	0.40%	0.41%	6.64%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	78.90%	5.60%	15.56%	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
vg0819104472	T -> C	LOC_Os08g30940.1	missense_variant ; p.Cys96Arg; MODERATE	nonsynonymous_codon ; C96H	Average:24.421; most accessible tissue: Minghui63 root, score: 35.002	unknown	unknown	TOLERATED	0.56
vg0819104472	T -> C	LOC_Os08g30940.1	missense_variant ; p.Cys96Arg; MODERATE	nonsynonymous_codon ; C96R	Average:24.421; most accessible tissue: Minghui63 root, score: 35.002	unknown	unknown	TOLERATED	0.46
vg0819104472	T -> DEL	LOC_Os08g30940.1	N	frameshift_variant	Average:24.421; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819104472	NA	6.79E-06	mr1039	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
vg0819104472	NA	2.72E-23	mr1217	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
vg0819104472	4.74E-06	1.51E-09	mr1227	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
vg0819104472	NA	8.71E-29	mr1256	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
vg0819104472	7.19E-08	7.19E-08	mr1266	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
vg0819104472	NA	2.98E-09	mr1275	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
vg0819104472	NA	1.74E-10	mr1307	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
vg0819104472	NA	2.80E-06	mr1345	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
vg0819104472	NA	2.42E-12	mr1386	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
vg0819104472	NA	1.58E-08	mr1607	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
vg0819104472	NA	1.46E-06	mr1622	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
vg0819104472	NA	4.68E-06	mr1700	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
vg0819104472	NA	2.13E-21	mr1845	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
vg0819104472	NA	1.25E-06	mr1881	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
vg0819104472	NA	1.34E-13	mr1940	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
vg0819104472	NA	5.46E-08	mr1047_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
vg0819104472	4.47E-06	NA	mr1520_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