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Detailed information for vg0404302990:

Variant ID: vg0404302990 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4302990
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATAGAGTTTTAATAGTGACATGATAATTAATTTTGTAGTATTTTTAAGGCCCAATGTATTATATCCCTTGCAAGAATGGCATCGTGGAAAAAATACAT[C/T]
TTCACGGCTTAAAAAGACATATTGCTCTAACTAGGTTTTAGCCGCTAAAATCATAAGAACTAAAGGAGACCAAAATAATGACGCTAAAAAAAAACTCGAG

Reverse complement sequence

CTCGAGTTTTTTTTTAGCGTCATTATTTTGGTCTCCTTTAGTTCTTATGATTTTAGCGGCTAAAACCTAGTTAGAGCAATATGTCTTTTTAAGCCGTGAA[G/A]
ATGTATTTTTTCCACGATGCCATTCTTGCAAGGGATATAATACATTGGGCCTTAAAAATACTACAAAATTAATTATCATGTCACTATTAAAACTCTATGT

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	91.90%	8.00%	0.11%	0.00%	NA
All Indica	2759	93.50%	6.40%	0.11%	0.00%	NA
All Japonica	1512	91.90%	8.00%	0.07%	0.00%	NA
Aus	269	75.80%	23.80%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	93.80%	6.20%	0.00%	0.00%	NA
Indica III	913	88.80%	11.00%	0.22%	0.00%	NA
Indica Intermediate	786	93.80%	6.10%	0.13%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	89.70%	10.30%	0.00%	0.00%	NA
Japonica Intermediate	241	74.70%	24.90%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0404302990	C -> T	LOC_Os04g08060-LOC_Os04g08070	intergenic_region ; MODIFIER	silent_mutation	Average:76.732; most accessible tissue: Callus, score: 91.717	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404302990	8.55E-07	NA	mr1695_2	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