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Detailed information for vg0825541162:

Variant ID: vg0825541162 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25541162
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.30, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GTCGGCGAACGAGCGTGCCGACAAGCTGGAACGCGACCTGGCGGAGGTTCGCGAGGACCTCCAGAAGATGAGGGAGCTGGTGGCCGGTAACGAGCGGCAA[T/C]
GGCGGGGACTCGAGGACCGGATGTCGGAACTCAAGAACAACCTGTCGGGGATCCGTGGGTCGCTGCGGGTCACCTACACCGGTCTTCATCAGCTCGCCGG

Reverse complement sequence

CCGGCGAGCTGATGAAGACCGGTGTAGGTGACCCGCAGCGACCCACGGATCCCCGACAGGTTGTTCTTGAGTTCCGACATCCGGTCCTCGAGTCCCCGCC[A/G]
TTGCCGCTCGTTACCGGCCACCAGCTCCCTCATCTTCTGGAGGTCCTCGCGAACCTCCGCCAGGTCGCGTTCCAGCTTGTCGGCACGCTCGTTCGCCGAC

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	47.60%	36.60%	0.68%	15.17%	NA
All Indica	2759	26.50%	47.50%	1.01%	25.01%	NA
All Japonica	1512	74.10%	24.60%	0.26%	0.99%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	45.70%	21.80%	1.18%	31.26%	NA
Indica II	465	18.50%	28.40%	2.80%	50.32%	NA
Indica III	913	18.50%	78.50%	0.00%	2.96%	NA
Indica Intermediate	786	26.00%	42.10%	1.02%	30.92%	NA
Temperate Japonica	767	64.30%	34.20%	0.26%	1.30%	NA
Tropical Japonica	504	95.60%	4.00%	0.20%	0.20%	NA
Japonica Intermediate	241	60.60%	37.30%	0.41%	1.66%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	52.20%	34.40%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0825541162	T -> C	LOC_Os08g40340.1	missense_variant ; p.Trp437Arg; MODERATE	nonsynonymous_codon ; W437R	Average:24.024; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	unknown	unknown	TOLERATED	1.00
vg0825541162	T -> DEL	LOC_Os08g40340.1	N	frameshift_variant	Average:24.024; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825541162	NA	3.68E-06	mr1230	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
vg0825541162	NA	5.52E-07	mr1382	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
vg0825541162	NA	1.33E-07	mr1382	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
vg0825541162	NA	1.43E-06	mr1518	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
vg0825541162	NA	2.45E-07	mr1676	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
vg0825541162	NA	4.19E-10	mr1696	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
vg0825541162	NA	6.11E-07	mr1696	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
vg0825541162	NA	7.64E-06	mr1707	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
vg0825541162	NA	3.90E-06	mr1807	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
vg0825541162	8.72E-08	3.83E-12	mr1874	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
vg0825541162	NA	3.75E-06	mr1786_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
vg0825541162	8.93E-10	NA	mr1874_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
vg0825541162	3.25E-11	1.77E-17	mr1874_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