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Detailed information for vg0814635395:

Variant ID: vg0814635395 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 14635395
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGGTTCTAAGCTGAACTTTAGTACTGCTTATCATCCGCAAACAGACGGACAAACCGAAAGGGTGAATCAGATTTTGGAAGACATGTTGAGAGCTTGTG[T/C]
TTTAGACTTCGGTGGAAGTTGGGATAAGAATCTACCTTATGCGGAATTCTCGTACAACAACAGTTATCAAGCTAGTCTTCAGATGGCTCCTTACGAAGCA

Reverse complement sequence

TGCTTCGTAAGGAGCCATCTGAAGACTAGCTTGATAACTGTTGTTGTACGAGAATTCCGCATAAGGTAGATTCTTATCCCAACTTCCACCGAAGTCTAAA[A/G]
CACAAGCTCTCAACATGTCTTCCAAAATCTGATTCACCCTTTCGGTTTGTCCGTCTGTTTGCGGATGATAAGCAGTACTAAAGTTCAGCTTAGAACCCAT

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	9.60%	0.30%	25.33%	64.75%	NA
All Indica	2759	5.30%	0.30%	27.40%	66.94%	NA
All Japonica	1512	18.50%	0.40%	21.10%	59.99%	NA
Aus	269	3.00%	0.00%	10.04%	86.99%	NA
Indica I	595	5.70%	0.00%	11.93%	82.35%	NA
Indica II	465	3.90%	0.00%	13.76%	82.37%	NA
Indica III	913	6.70%	1.00%	47.10%	45.24%	NA
Indica Intermediate	786	4.30%	0.00%	24.30%	71.37%	NA
Temperate Japonica	767	32.90%	0.00%	1.56%	65.58%	NA
Tropical Japonica	504	2.40%	1.00%	51.19%	45.44%	NA
Japonica Intermediate	241	6.60%	0.40%	20.33%	72.61%	NA
VI/Aromatic	96	3.10%	0.00%	67.71%	29.17%	NA
Intermediate	90	17.80%	0.00%	33.33%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0814635395	T -> C	LOC_Os08g24240.1	missense_variant ; p.Val169Ala; MODERATE	nonsynonymous_codon ; V169A	Average:12.398; most accessible tissue: Zhenshan97 panicle, score: 16.188	benign	-0.571	TOLERATED	1.00
vg0814635395	T -> DEL	LOC_Os08g24240.1	N	frameshift_variant	Average:12.398; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0814635395	2.81E-06	2.81E-06	mr1175	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
vg0814635395	NA	9.85E-06	mr1117_2	Jap_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