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Detailed information for vg0911764924:

Variant ID: vg0911764924 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11764924
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAGTTTAGAGTAAATTGCACCCACAGTACAACAACTTGGCAGGTGGGTGCGATATAGTGAAAGAACTTGAGAATTGAACGTCCGAGTGCAACATAATGA[C/T]
AAGTGGGTGCGTTCTACTATAAGAACTTGACAATTTAATATTTTGGTGCATCAACTTGGCTAAGCATATGCTAGCTGAGTTTTTTTCACGATGTAAATAT

Reverse complement sequence

ATATTTACATCGTGAAAAAAACTCAGCTAGCATATGCTTAGCCAAGTTGATGCACCAAAATATTAAATTGTCAAGTTCTTATAGTAGAACGCACCCACTT[G/A]
TCATTATGTTGCACTCGGACGTTCAATTCTCAAGTTCTTTCACTATATCGCACCCACCTGCCAAGTTGTTGTACTGTGGGTGCAATTTACTCTAAACTTA

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%	9.60%	0.34%	1.02%	NA
All Indica	2759	83.50%	14.30%	0.58%	1.59%	NA
All Japonica	1512	99.30%	0.60%	0.00%	0.07%	NA
Aus	269	81.80%	17.50%	0.00%	0.74%	NA
Indica I	595	95.60%	4.40%	0.00%	0.00%	NA
Indica II	465	86.90%	10.30%	0.43%	2.37%	NA
Indica III	913	72.00%	23.30%	1.42%	3.29%	NA
Indica Intermediate	786	85.80%	13.70%	0.13%	0.38%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911764924	C -> DEL	N	N	silent_mutation	Average:45.757; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0911764924	C -> T	LOC_Os09g19670.1	upstream_gene_variant ; 2804.0bp to feature; MODIFIER	silent_mutation	Average:45.757; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0911764924	C -> T	LOC_Os09g19650-LOC_Os09g19670	intergenic_region ; MODIFIER	silent_mutation	Average:45.757; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911764924	2.93E-06	5.20E-06	mr1388_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