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Detailed information for vg0904631897:

Variant ID: vg0904631897 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 4631897
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCGGCTAGAGGGCTAAATAACTTTGAAGCTTTACAGAAGGCAGCAAAGGAAGTTTTGTACGATGTGTCGAAGGGCTGTGACAGTAAGTTCACAGCACTC[T/C]
GGTCAGTTCTTGAACTTATGAGGTTAAAGGCGAGACATGGATGGTCTGATACCAGTTTCGACAGTCTGTTAGAACTTCTGCAGAAAATGCTACCGAGGCC

Reverse complement sequence

GGCCTCGGTAGCATTTTCTGCAGAAGTTCTAACAGACTGTCGAAACTGGTATCAGACCATCCATGTCTCGCCTTTAACCTCATAAGTTCAAGAACTGACC[A/G]
GAGTGCTGTGAACTTACTGTCACAGCCCTTCGACACATCGTACAAAACTTCCTTTGCTGCCTTCTGTAAAGCTTCAAAGTTATTTAGCCCTCTAGCCGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.10%	0.10%	11.49%	10.28%	NA
All Indica	2759	82.80%	0.30%	12.76%	4.17%	NA
All Japonica	1512	66.50%	0.00%	10.12%	23.35%	NA
Aus	269	96.70%	0.00%	3.35%	0.00%	NA
Indica I	595	72.80%	0.20%	19.50%	7.56%	NA
Indica II	465	84.70%	0.00%	11.18%	4.09%	NA
Indica III	913	87.50%	0.40%	10.73%	1.31%	NA
Indica Intermediate	786	83.80%	0.30%	10.94%	4.96%	NA
Temperate Japonica	767	98.30%	0.00%	0.52%	1.17%	NA
Tropical Japonica	504	20.40%	0.00%	25.20%	54.37%	NA
Japonica Intermediate	241	61.80%	0.00%	9.13%	29.05%	NA
VI/Aromatic	96	77.10%	0.00%	15.62%	7.29%	NA
Intermediate	90	72.20%	0.00%	15.56%	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
vg0904631897	T -> DEL	LOC_Os09g08780.1	N	frameshift_variant	Average:23.764; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg0904631897	T -> C	LOC_Os09g08780.1	missense_variant ; p.Trp160Arg; MODERATE	nonsynonymous_codon ; W160R	Average:23.764; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0904631897	6.42E-06	9.71E-07	mr1708_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