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Detailed information for vg0324319095:

Variant ID: vg0324319095 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24319095
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGATCCATCAAAAACTTTTATGAGTTCTTAAATTAACCACTGCATGCAATGCTTCTTCTTCTCCTTCTCCTTCATGTTCTTCTTCTTGTTCACGTCATC[A/C]
TCTTTGACTCTCCCATCATCTTCCTTCTTGCCTCTCCCAAGCTTCGGACAATGCGAGCGAAGATGATCAAGTGCTCCACACTCAAAACAACGATTCGGTT

Reverse complement sequence

AACCGAATCGTTGTTTTGAGTGTGGAGCACTTGATCATCTTCGCTCGCATTGTCCGAAGCTTGGGAGAGGCAAGAAGGAAGATGATGGGAGAGTCAAAGA[T/G]
GATGACGTGAACAAGAAGAAGAACATGAAGGAGAAGGAGAAGAAGAAGCATTGCATGCAGTGGTTAATTTAAGAACTCATAAAAGTTTTTGATGGATCTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.10%	1.00%	37.64%	8.27%	NA
All Indica	2759	25.50%	1.50%	60.49%	12.47%	NA
All Japonica	1512	99.30%	0.00%	0.53%	0.13%	NA
Aus	269	51.30%	2.20%	31.23%	15.24%	NA
Indica I	595	17.30%	0.50%	60.67%	21.51%	NA
Indica II	465	21.50%	1.10%	61.72%	15.70%	NA
Indica III	913	30.00%	3.00%	61.77%	5.26%	NA
Indica Intermediate	786	28.90%	0.90%	58.14%	12.09%	NA
Temperate Japonica	767	99.50%	0.00%	0.52%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	98.80%	0.00%	1.24%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	76.70%	0.00%	18.89%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0324319095	A -> C	LOC_Os03g43550.1	intron_variant ; MODIFIER	silent_mutation	Average:8.024; most accessible tissue: Zhenshan97 flower, score: 12.818	N	N	N	N
vg0324319095	A -> DEL	N	N	silent_mutation	Average:8.024; most accessible tissue: Zhenshan97 flower, score: 12.818	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324319095	7.02E-06	7.01E-06	mr1240	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