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Detailed information for vg0907966825:

Variant ID: vg0907966825 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7966825
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTAGTACAGAAGTGTAGGCCTCACTCCTGTGTGTATAACAGAATATATAATGCAAATATTAATTATTATTACTGACAACATATATATATATATATATA[C/T]
AGCCGGGTGATAAGCGTAGTAAAAACTCTTTTAAAAAAGTACGCAGTAAAAGGATTGGAGAAGGATGAAACAAAACTTGATGATGAGTTGCTAGCTGGAC

Reverse complement sequence

GTCCAGCTAGCAACTCATCATCAAGTTTTGTTTCATCCTTCTCCAATCCTTTTACTGCGTACTTTTTTAAAAGAGTTTTTACTACGCTTATCACCCGGCT[G/A]
TATATATATATATATATATGTTGTCAGTAATAATAATTAATATTTGCATTATATATTCTGTTATACACACAGGAGTGAGGCCTACACTTCTGTACTAAGA

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	89.00%	10.20%	0.72%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.00%	0.00%	NA
All Japonica	1512	74.50%	23.30%	2.12%	0.00%	NA
Aus	269	95.50%	4.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.30%	0.00%	0.00%	NA
Temperate Japonica	767	96.90%	2.30%	0.78%	0.00%	NA
Tropical Japonica	504	35.30%	60.50%	4.17%	0.00%	NA
Japonica Intermediate	241	85.50%	12.40%	2.07%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	73.30%	24.40%	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
vg0907966825	C -> T	LOC_Os09g13650.2	3_prime_UTR_variant ; 150.0bp to feature; MODIFIER	silent_mutation	Average:39.447; most accessible tissue: Callus, score: 74.422	N	N	N	N
vg0907966825	C -> T	LOC_Os09g13650.3	3_prime_UTR_variant ; 561.0bp to feature; MODIFIER	silent_mutation	Average:39.447; most accessible tissue: Callus, score: 74.422	N	N	N	N
vg0907966825	C -> T	LOC_Os09g13650.1	intron_variant ; MODIFIER	silent_mutation	Average:39.447; most accessible tissue: Callus, score: 74.422	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907966825	2.80E-06	NA	mr1295	Jap_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