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Detailed information for vg0402374019:

Variant ID: vg0402374019 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2374019
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCTTACCTAAGATCGCCAGAATCGCCACCGCCATGGCCGCCTCCGCCTCCTGCTCGTGCCCGCGCCGCCAACATCACCGCCGGCGCACCATGCCTCCGC[T/C]
GGCCACGAGATTAGGGTCGCCGCACCCTGGGGACCCCAAAACCGGCGCCATTCTGATGAAAACCGGCCTCCTCCTCCGCCGGCGTCGGCTCCTATGCAGA

Reverse complement sequence

TCTGCATAGGAGCCGACGCCGGCGGAGGAGGAGGCCGGTTTTCATCAGAATGGCGCCGGTTTTGGGGTCCCCAGGGTGCGGCGACCCTAATCTCGTGGCC[A/G]
GCGGAGGCATGGTGCGCCGGCGGTGATGTTGGCGGCGCGGGCACGAGCAGGAGGCGGAGGCGGCCATGGCGGTGGCGATTCTGGCGATCTTAGGTAAGGG

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	83.30%	16.50%	0.17%	0.00%	NA
All Indica	2759	83.30%	16.60%	0.04%	0.00%	NA
All Japonica	1512	84.00%	15.60%	0.40%	0.00%	NA
Aus	269	88.80%	11.20%	0.00%	0.00%	NA
Indica I	595	97.60%	2.40%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	66.80%	33.20%	0.00%	0.00%	NA
Indica Intermediate	786	83.20%	16.70%	0.13%	0.00%	NA
Temperate Japonica	767	97.30%	2.60%	0.13%	0.00%	NA
Tropical Japonica	504	73.40%	26.00%	0.60%	0.00%	NA
Japonica Intermediate	241	63.90%	35.30%	0.83%	0.00%	NA
VI/Aromatic	96	53.10%	46.90%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	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
vg0402374019	T -> C	LOC_Os04g04930.1	upstream_gene_variant ; 459.0bp to feature; MODIFIER	silent_mutation	Average:51.725; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N
vg0402374019	T -> C	LOC_Os04g04914.1	downstream_gene_variant ; 1760.0bp to feature; MODIFIER	silent_mutation	Average:51.725; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N
vg0402374019	T -> C	LOC_Os04g04914-LOC_Os04g04930	intergenic_region ; MODIFIER	silent_mutation	Average:51.725; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402374019	2.51E-08	NA	mr1037	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
vg0402374019	7.79E-07	7.26E-11	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
vg0402374019	4.46E-10	NA	mr1798	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
vg0402374019	1.77E-10	7.70E-18	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
vg0402374019	2.20E-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
vg0402374019	3.11E-08	2.15E-10	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
vg0402374019	NA	8.56E-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
vg0402374019	6.81E-22	NA	mr1798_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
vg0402374019	2.38E-19	1.08E-35	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
vg0402374019	1.19E-06	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