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Detailed information for vg0910207948:

Variant ID: vg0910207948 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10207948
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGATTGGGATAGATTGGTCGCTATGCCGAGATAGTATAAATCACTTAGATCGAAATATATATTAACAACAGGACTATATATGTTCATAGCATAGCCGAT[T/C]
AGATGGATCTAGCGTGTATCGGCTAATACTCCGATACCACTCTATATTAAGATATCAAAACAAGTAAAATATACCAAACAAAGGCCTAATATACTTAAAT

Reverse complement sequence

ATTTAAGTATATTAGGCCTTTGTTTGGTATATTTTACTTGTTTTGATATCTTAATATAGAGTGGTATCGGAGTATTAGCCGATACACGCTAGATCCATCT[A/G]
ATCGGCTATGCTATGAACATATATAGTCCTGTTGTTAATATATATTTCGATCTAAGTGATTTATACTATCTCGGCATAGCGACCAATCTATCCCAATCAC

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	69.40%	16.90%	0.11%	13.54%	NA
All Indica	2759	75.80%	2.80%	0.18%	21.24%	NA
All Japonica	1512	55.10%	43.30%	0.00%	1.59%	NA
Aus	269	94.40%	1.10%	0.00%	4.46%	NA
Indica I	595	93.10%	6.70%	0.00%	0.17%	NA
Indica II	465	53.50%	3.70%	0.65%	42.15%	NA
Indica III	913	73.50%	0.30%	0.11%	26.07%	NA
Indica Intermediate	786	78.40%	2.30%	0.13%	19.21%	NA
Temperate Japonica	767	30.60%	69.10%	0.00%	0.26%	NA
Tropical Japonica	504	86.50%	9.30%	0.00%	4.17%	NA
Japonica Intermediate	241	67.20%	32.40%	0.00%	0.41%	NA
VI/Aromatic	96	52.10%	40.60%	0.00%	7.29%	NA
Intermediate	90	60.00%	27.80%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910207948	T -> DEL	N	N	silent_mutation	Average:29.687; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N
vg0910207948	T -> C	LOC_Os09g16650.1	upstream_gene_variant ; 3091.0bp to feature; MODIFIER	silent_mutation	Average:29.687; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N
vg0910207948	T -> C	LOC_Os09g16660.1	intron_variant ; MODIFIER	silent_mutation	Average:29.687; most accessible tissue: Zhenshan97 root, score: 47.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910207948	3.19E-06	NA	mr1083_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
vg0910207948	NA	5.22E-06	mr1763_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