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Detailed information for vg0402406368:

Variant ID: vg0402406368 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2406368
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATACACACAGTGTCTTGGAGTCTGTGCTACAGCTGGCTATAAATCTGTAGCCCGCTGCCCTTATATCTCCTTATTTATCTCTTTAAAATATGTTTGCAG[C/T]
TGGCTTATAGCCTGCTATTGTACCTGCTCTAAAAGGTGCTTCCCCAAGCTAAAAATCGGACAAAGAGAGCCATCATTTCGCTTATGCTTATACTTATAAA

Reverse complement sequence

TTTATAAGTATAAGCATAAGCGAAATGATGGCTCTCTTTGTCCGATTTTTAGCTTGGGGAAGCACCTTTTAGAGCAGGTACAATAGCAGGCTATAAGCCA[G/A]
CTGCAAACATATTTTAAAGAGATAAATAAGGAGATATAAGGGCAGCGGGCTACAGATTTATAGCCAGCTGTAGCACAGACTCCAAGACACTGTGTGTATA

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	82.00%	15.90%	0.04%	2.05%	NA
All Indica	2759	82.90%	17.10%	0.00%	0.00%	NA
All Japonica	1512	77.50%	16.50%	0.07%	5.95%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	94.30%	5.70%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	69.20%	30.80%	0.00%	0.00%	NA
Indica Intermediate	786	81.30%	18.70%	0.00%	0.00%	NA
Temperate Japonica	767	94.50%	2.10%	0.13%	3.26%	NA
Tropical Japonica	504	53.80%	35.30%	0.00%	10.91%	NA
Japonica Intermediate	241	73.00%	22.80%	0.00%	4.15%	NA
VI/Aromatic	96	90.60%	4.20%	0.00%	5.21%	NA
Intermediate	90	81.10%	15.60%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402406368	C -> DEL	N	N	silent_mutation	Average:43.384; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0402406368	C -> T	LOC_Os04g04970.1	upstream_gene_variant ; 1657.0bp to feature; MODIFIER	silent_mutation	Average:43.384; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0402406368	C -> T	LOC_Os04g04950-LOC_Os04g04970	intergenic_region ; MODIFIER	silent_mutation	Average:43.384; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402406368	5.41E-06	NA	mr1037	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
vg0402406368	1.81E-06	1.26E-12	mr1037	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
vg0402406368	NA	1.09E-11	mr1410	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
vg0402406368	2.34E-15	NA	mr1798	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
vg0402406368	7.15E-12	1.48E-19	mr1798	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
vg0402406368	8.88E-08	NA	mr1037_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
vg0402406368	2.68E-08	4.53E-12	mr1037_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
vg0402406368	NA	1.40E-07	mr1158_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
vg0402406368	NA	6.35E-06	mr1181_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
vg0402406368	NA	9.32E-13	mr1410_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
vg0402406368	1.23E-32	NA	mr1798_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
vg0402406368	3.26E-16	2.27E-39	mr1798_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
vg0402406368	1.42E-11	NA	mr1798_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