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Detailed information for vg0720001039:

Variant ID: vg0720001039 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20001039
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGTTTTGTGAACCTTGGATGTACCGATGGACTGACTAAAACAATTAATTAAAGAATTACTCCATGCCTAAAACCATTTTATTTTATCCATCAGTTTGGC[C/T]
GGCCTCACGTACGGCCGGCACAAGTGCACAACATACAGGTACATGCATGCATCCAACGGCGGAGCCAGCGTGGGGGGGGGGGAGAGGGAGAGGAAGAAGA

Reverse complement sequence

TCTTCTTCCTCTCCCTCTCCCCCCCCCCCACGCTGGCTCCGCCGTTGGATGCATGCATGTACCTGTATGTTGTGCACTTGTGCCGGCCGTACGTGAGGCC[G/A]
GCCAAACTGATGGATAAAATAAAATGGTTTTAGGCATGGAGTAATTCTTTAATTAATTGTTTTAGTCAGTCCATCGGTACATCCAAGGTTCACAAAACGC

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	90.10%	6.60%	0.08%	3.24%	NA
All Indica	2759	92.40%	7.60%	0.04%	0.00%	NA
All Japonica	1512	89.40%	0.50%	0.20%	9.99%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.60%	9.40%	0.00%	0.00%	NA
Indica II	465	88.60%	11.20%	0.22%	0.00%	NA
Indica III	913	97.80%	2.20%	0.00%	0.00%	NA
Indica Intermediate	786	89.70%	10.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	70.00%	0.00%	0.60%	29.37%	NA
Japonica Intermediate	241	96.30%	2.50%	0.00%	1.24%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	85.60%	12.20%	0.00%	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
vg0720001039	C -> DEL	N	N	silent_mutation	Average:55.898; most accessible tissue: Zhenshan97 young leaf, score: 74.675	N	N	N	N
vg0720001039	C -> T	LOC_Os07g33470.1	upstream_gene_variant ; 2440.0bp to feature; MODIFIER	silent_mutation	Average:55.898; most accessible tissue: Zhenshan97 young leaf, score: 74.675	N	N	N	N
vg0720001039	C -> T	LOC_Os07g33450.1	downstream_gene_variant ; 4683.0bp to feature; MODIFIER	silent_mutation	Average:55.898; most accessible tissue: Zhenshan97 young leaf, score: 74.675	N	N	N	N
vg0720001039	C -> T	LOC_Os07g33460.1	downstream_gene_variant ; 726.0bp to feature; MODIFIER	silent_mutation	Average:55.898; most accessible tissue: Zhenshan97 young leaf, score: 74.675	N	N	N	N
vg0720001039	C -> T	LOC_Os07g33460-LOC_Os07g33470	intergenic_region ; MODIFIER	silent_mutation	Average:55.898; most accessible tissue: Zhenshan97 young leaf, score: 74.675	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720001039	2.60E-06	NA	mr1188_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
vg0720001039	NA	3.07E-07	mr1188_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