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Detailed information for vg0325762988:

Variant ID: vg0325762988 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 25762988
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTATAATGGCGTGGCTTGTGTCTCGTAGATGCGTCTCACCGTCTCCTCCAGGGTAGTCCAACTCGAGGACCTCGTACGCGGCTTCCACCAGCTCAACTT[T/C]
GACCCTCGAGTATCCTGCTGGAATCGGCCTGCAATGGTAAGTCCCTGAAGGGTCCGTTGGGATGGTCATTCCCAACGCCACCTTCACATGATGAGAGGTT

Reverse complement sequence

AACCTCTCATCATGTGAAGGTGGCGTTGGGAATGACCATCCCAACGGACCCTTCAGGGACTTACCATTGCAGGCCGATTCCAGCAGGATACTCGAGGGTC[A/G]
AAGTTGAGCTGGTGGAAGCCGCGTACGAGGTCCTCGAGTTGGACTACCCTGGAGGAGACGGTGAGACGCATCTACGAGACACAAGCCACGCCATTATACT

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	85.40%	13.90%	0.42%	0.34%	NA
All Indica	2759	96.70%	2.80%	0.00%	0.58%	NA
All Japonica	1512	70.40%	29.50%	0.07%	0.00%	NA
Aus	269	75.10%	24.90%	0.00%	0.00%	NA
Indica I	595	96.10%	1.50%	0.00%	2.35%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.50%	0.40%	0.00%	0.11%	NA
Indica Intermediate	786	92.10%	7.80%	0.00%	0.13%	NA
Temperate Japonica	767	72.00%	28.00%	0.00%	0.00%	NA
Tropical Japonica	504	74.40%	25.60%	0.00%	0.00%	NA
Japonica Intermediate	241	57.30%	42.30%	0.41%	0.00%	NA
VI/Aromatic	96	30.20%	52.10%	17.71%	0.00%	NA
Intermediate	90	78.90%	18.90%	2.22%	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
vg0325762988	T -> C	LOC_Os03g45650.1	missense_variant ; p.Lys99Glu; MODERATE	nonsynonymous_codon ; K99E	Average:63.245; most accessible tissue: Zhenshan97 young leaf, score: 80.056	benign	-0.481	TOLERATED	1.00
vg0325762988	T -> DEL	LOC_Os03g45650.1	N	frameshift_variant	Average:63.245; most accessible tissue: Zhenshan97 young leaf, score: 80.056	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0325762988	6.27E-06	1.04E-06	mr1305	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
vg0325762988	8.53E-06	NA	mr1585	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
vg0325762988	4.65E-06	3.01E-06	mr1586	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
vg0325762988	NA	3.00E-06	mr1765	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
vg0325762988	1.11E-06	NA	mr1305_2	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
vg0325762988	5.68E-06	7.66E-06	mr1409_2	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
vg0325762988	9.96E-06	NA	mr1585_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