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Detailed information for vg0900683858:

Variant ID: vg0900683858 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 683858
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCGATCAACCCTTTTATGGAATCACTCCCCAATCCTCGTCTAGACCATTGGGCAATATTACGTTGCCTGTGACTTTCGGCCAAGCTAACAACTTCCAAA[C/T]
GGAGCAGATCGCCTTTGATGTCGCTGAATTCGATACAGCTTACAACGCCATCATCGGGAGAACTGCACTTGCAAAGTTTATGGCCGCATCTCACTACGCG

Reverse complement sequence

CGCGTAGTGAGATGCGGCCATAAACTTTGCAAGTGCAGTTCTCCCGATGATGGCGTTGTAAGCTGTATCGAATTCAGCGACATCAAAGGCGATCTGCTCC[G/A]
TTTGGAAGTTGTTAGCTTGGCCGAAAGTCACAGGCAACGTAATATTGCCCAATGGTCTAGACGAGGATTGGGGAGTGATTCCATAAAAGGGTTGATCGGT

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	87.20%	3.50%	8.29%	1.08%	NA
All Indica	2759	78.60%	5.90%	13.63%	1.85%	NA
All Japonica	1512	99.90%	0.00%	0.13%	0.00%	NA
Aus	269	95.20%	0.00%	4.83%	0.00%	NA
Indica I	595	53.30%	11.90%	33.78%	1.01%	NA
Indica II	465	87.50%	2.80%	6.67%	3.01%	NA
Indica III	913	90.50%	4.10%	2.96%	2.52%	NA
Indica Intermediate	786	78.80%	5.30%	14.89%	1.02%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	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	97.80%	1.10%	1.11%	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
vg0900683858	C -> DEL	LOC_Os09g01980.1	N	frameshift_variant	Average:39.611; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N
vg0900683858	C -> T	LOC_Os09g01980.1	missense_variant ; p.Thr463Met; MODERATE	nonsynonymous_codon ; T463M	Average:39.611; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	benign	1.152	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900683858	2.39E-06	NA	mr1711	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
vg0900683858	NA	7.65E-06	mr1711	Ind_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