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Detailed information for vg0324994125:

Variant ID: vg0324994125 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24994125
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCATTTTCTTAGGTAATGGAAATGAATTATATTTCCGGCCTCTATCCGTGGACACACAGCCAAAAAGTCTTAGAAGTAAATAGGAAGAAATTAAAAAA[G/T]
GCGTGATGTGACAAACCTCCCAACTTCCGTCAATAAAATGATCGACTAAAATAATGTTTCCAAAATCATATAGATTCTAGAACAACATTTTGTAGGTACT

Reverse complement sequence

AGTACCTACAAAATGTTGTTCTAGAATCTATATGATTTTGGAAACATTATTTTAGTCGATCATTTTATTGACGGAAGTTGGGAGGTTTGTCACATCACGC[C/A]
TTTTTTAATTTCTTCCTATTTACTTCTAAGACTTTTTGGCTGTGTGTCCACGGATAGAGGCCGGAAATATAATTCATTTCCATTACCTAAGAAAATGGAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.60%	3.30%	0.06%	0.00%	NA
All Indica	2759	94.60%	5.40%	0.00%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.20%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	88.90%	11.10%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	96.70%	3.30%	0.00%	0.00%	NA
Indica Intermediate	786	93.40%	6.60%	0.00%	0.00%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0324994125	G -> T	LOC_Os03g44410.1	upstream_gene_variant ; 737.0bp to feature; MODIFIER	silent_mutation	Average:45.816; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0324994125	G -> T	LOC_Os03g44420.1	upstream_gene_variant ; 2451.0bp to feature; MODIFIER	silent_mutation	Average:45.816; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0324994125	G -> T	LOC_Os03g44400-LOC_Os03g44410	intergenic_region ; MODIFIER	silent_mutation	Average:45.816; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324994125	1.75E-06	7.12E-07	mr1097_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