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Detailed information for vg0404528034:

Variant ID: vg0404528034 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4528034
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCGGAGGCAGGCGCGACGTGGGAACATGGCTGTCTGCTGGCGACATGACCAGTGTCAGACCGGTCACAAATCGGTCATTCTTGTCCACCACATGTCAGT[T/C]
TAACAATCTGCATGTTCGCCCTTCTTCATACAATATCTTGCCTGTAATGGTTAGGATATATCTGACCGGGTCCAACGTGCCACCTCCAGGAGCTAACACG

Reverse complement sequence

CGTGTTAGCTCCTGGAGGTGGCACGTTGGACCCGGTCAGATATATCCTAACCATTACAGGCAAGATATTGTATGAAGAAGGGCGAACATGCAGATTGTTA[A/G]
ACTGACATGTGGTGGACAAGAATGACCGATTTGTGACCGGTCTGACACTGGTCATGTCGCCAGCAGACAGCCATGTTCCCACGTCGCGCCTGCCTCCGGC

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	17.60%	2.10%	16.91%	63.39%	NA
All Indica	2759	3.40%	3.50%	26.50%	66.58%	NA
All Japonica	1512	47.30%	0.10%	1.46%	51.19%	NA
Aus	269	1.10%	0.70%	8.92%	89.22%	NA
Indica I	595	2.90%	5.20%	9.58%	82.35%	NA
Indica II	465	5.60%	1.90%	36.34%	56.13%	NA
Indica III	913	1.60%	3.50%	31.98%	62.87%	NA
Indica Intermediate	786	4.70%	3.10%	27.10%	65.14%	NA
Temperate Japonica	767	82.80%	0.00%	0.26%	16.95%	NA
Tropical Japonica	504	5.20%	0.20%	3.77%	90.87%	NA
Japonica Intermediate	241	22.40%	0.00%	0.41%	77.18%	NA
VI/Aromatic	96	1.00%	0.00%	7.29%	91.67%	NA
Intermediate	90	17.80%	2.20%	16.67%	63.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404528034	T -> C	LOC_Os04g08430.1	upstream_gene_variant ; 1111.0bp to feature; MODIFIER	silent_mutation	Average:9.27; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0404528034	T -> C	LOC_Os04g08415-LOC_Os04g08430	intergenic_region ; MODIFIER	silent_mutation	Average:9.27; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N
vg0404528034	T -> DEL	N	N	silent_mutation	Average:9.27; most accessible tissue: Zhenshan97 root, score: 16.934	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404528034	2.86E-07	2.86E-07	mr1160	Ind_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