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Detailed information for vg0324941311:

Variant ID: vg0324941311 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24941311
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.26, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TCATATTAGCAATGATCTCACGTATCCAGAACACCCAGTCCGGATATTGGATGAAGCAGAAAAGAGGACTAGGACCAAAGTGTGGCGTATGTACAAGGTA[T/C]
AATAGAGTAATCACACTGAGGATGAGGCCACCTGGGAAAGCGAAGAATTCTTGAGGACAGAATACCCGCATCTATTCGAAAACTGGTAAGAAATCTCGGG

Reverse complement sequence

CCCGAGATTTCTTACCAGTTTTCGAATAGATGCGGGTATTCTGTCCTCAAGAATTCTTCGCTTTCCCAGGTGGCCTCATCCTCAGTGTGATTACTCTATT[A/G]
TACCTTGTACATACGCCACACTTTGGTCCTAGTCCTCTTTTCTGCTTCATCCAATATCCGGACTGGGTGTTCTGGATACGTGAGATCATTGCTAATATGA

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	81.70%	12.40%	5.90%	0.00%	NA
All Indica	2759	90.30%	6.40%	3.37%	0.00%	NA
All Japonica	1512	77.50%	10.80%	11.71%	0.00%	NA
Aus	269	15.60%	83.30%	1.12%	0.00%	NA
Indica I	595	88.10%	2.00%	9.92%	0.00%	NA
Indica II	465	96.30%	3.40%	0.22%	0.00%	NA
Indica III	913	87.40%	12.00%	0.55%	0.00%	NA
Indica Intermediate	786	91.60%	4.80%	3.56%	0.00%	NA
Temperate Japonica	767	63.90%	18.80%	17.34%	0.00%	NA
Tropical Japonica	504	93.50%	1.20%	5.36%	0.00%	NA
Japonica Intermediate	241	87.60%	5.40%	7.05%	0.00%	NA
VI/Aromatic	96	89.60%	9.40%	1.04%	0.00%	NA
Intermediate	90	78.90%	15.60%	5.56%	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
vg0324941311	T -> C	LOC_Os03g44360.1	stop_lost&splice_region_variant ; p.Ter1300Glnext*?; HIGH	stop_lost	Average:34.616; most accessible tissue: Minghui63 flag leaf, score: 61.847	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324941311	NA	3.63E-09	mr1388_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
vg0324941311	4.02E-06	NA	mr1705_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