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Detailed information for vg0907502049:

Variant ID: vg0907502049 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7502049
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAAGGGTTGGTATCATGCACGATTTGAAGGACCACCACCTAATCACAAACAAAACCTCAGCAAACACATTCAAACATGCATATAAAACATTGAAAAAGG[T/A]
GAACCTACTGGCCCATCCCATTACAACGCAATAACAAGGAACGCCGCTTGGACTATAAACAAGAATGCTGCTTCAAACCTTTATATCTTGAAATATGAAA

Reverse complement sequence

TTTCATATTTCAAGATATAAAGGTTTGAAGCAGCATTCTTGTTTATAGTCCAAGCGGCGTTCCTTGTTATTGCGTTGTAATGGGATGGGCCAGTAGGTTC[A/T]
CCTTTTTCAATGTTTTATATGCATGTTTGAATGTGTTTGCTGAGGTTTTGTTTGTGATTAGGTGGTGGTCCTTCAAATCGTGCATGATACCAACCCTTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.50%	8.10%	0.83%	30.66%	NA
All Indica	2759	51.90%	8.60%	1.09%	38.42%	NA
All Japonica	1512	80.30%	0.20%	0.46%	19.05%	NA
Aus	269	18.20%	49.40%	0.74%	31.60%	NA
Indica I	595	40.50%	3.50%	0.84%	55.13%	NA
Indica II	465	78.70%	5.40%	0.65%	15.27%	NA
Indica III	913	48.00%	12.80%	1.53%	37.68%	NA
Indica Intermediate	786	49.10%	9.50%	1.02%	40.33%	NA
Temperate Japonica	767	92.70%	0.10%	0.26%	6.91%	NA
Tropical Japonica	504	76.40%	0.20%	0.40%	23.02%	NA
Japonica Intermediate	241	49.00%	0.40%	1.24%	49.38%	NA
VI/Aromatic	96	95.80%	1.00%	0.00%	3.12%	NA
Intermediate	90	78.90%	6.70%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907502049	T -> DEL	N	N	silent_mutation	Average:18.2; most accessible tissue: Minghui63 flag leaf, score: 33.603	N	N	N	N
vg0907502049	T -> A	LOC_Os09g12990-LOC_Os09g13000	intergenic_region ; MODIFIER	silent_mutation	Average:18.2; most accessible tissue: Minghui63 flag leaf, score: 33.603	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907502049	5.66E-06	NA	mr1570	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