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Detailed information for vg0905249395:

Variant ID: vg0905249395 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5249395
Reference Allele: A	Alternative Allele: T,C
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGTACAAGGTTGAGGCATTATCTATTATCTAACGAGTGCACCGTTATATGCAAAGCCGATGTAGTCAGGTACATGCTATCGGCTCCAATATTAAAGGGA[A/T,C]
GAGTTGGAAAGTGGATATTTTCCTTGACTGAGTTTGATCTTTGGTATGAATCACCGAAGGCGATTAAGGGACAAGCTATAGCCGATTTTATTGTAGAACA

Reverse complement sequence

TGTTCTACAATAAAATCGGCTATAGCTTGTCCCTTAATCGCCTTCGGTGATTCATACCAAAGATCAAACTCAGTCAAGGAAAATATCCACTTTCCAACTC[T/A,G]
TCCCTTTAATATTGGAGCCGATAGCATGTACCTGACTACATCGGCTTTGCATATAACGGTGCACTCGTTAGATAATAGATAATGCCTCAACCTTGTACAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.80%	0.10%	0.06%	3.03%	C: 0.04%
All Indica	2759	99.70%	0.20%	0.07%	0.00%	C: 0.07%
All Japonica	1512	90.70%	0.00%	0.07%	9.26%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.50%	0.30%	0.11%	0.00%	C: 0.11%
Indica Intermediate	786	99.50%	0.30%	0.13%	0.00%	C: 0.13%
Temperate Japonica	767	95.20%	0.00%	0.00%	4.82%	NA
Tropical Japonica	504	95.20%	0.00%	0.00%	4.76%	NA
Japonica Intermediate	241	66.80%	0.00%	0.41%	32.78%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	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
vg0905249395	A -> DEL	LOC_Os09g09700.1	N	frameshift_variant	Average:21.345; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0905249395	A -> T	LOC_Os09g09700.1	stop_gained ; p.Arg592*; HIGH	stop_gained	Average:21.345; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0905249395	A -> C	LOC_Os09g09700.1	synonymous_variant ; p.Arg592Arg; LOW	synonymous_codon	Average:21.345; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905249395	2.95E-06	2.63E-06	mr1988	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