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Detailed information for vg0908678620:

Variant ID: vg0908678620 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 8678620
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, T: 0.23, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGAAATCAAATGGCAAATGACGCATGTGTGTTGATTTCACAGACTTAAACAAAGCATGTCCGAAGGACAATTTCCCCTTGCCGCGGATCGACCAGCTC[T/G]
TGGATTTGATAGCCGGCTGCAACTCATGAGCTTCCTAGATGCATATTCCGGCTATCACCAGATTCGCATGAACCCGGCCGACATCCCCAAGACAGCCATC

Reverse complement sequence

GATGGCTGTCTTGGGGATGTCGGCCGGGTTCATGCGAATCTGGTGATAGCCGGAATATGCATCTAGGAAGCTCATGAGTTGCAGCCGGCTATCAAATCCA[A/C]
GAGCTGGTCGATCCGCGGCAAGGGGAAATTGTCCTTCGGACATGCTTTGTTTAAGTCTGTGAAATCAACACACATGCGTCATTTGCCATTTGATTTCCGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.80%	36.60%	1.97%	20.57%	NA
All Indica	2759	59.80%	29.00%	2.25%	8.99%	NA
All Japonica	1512	9.80%	49.70%	0.73%	39.75%	NA
Aus	269	37.20%	13.00%	7.06%	42.75%	NA
Indica I	595	49.40%	12.10%	7.90%	30.59%	NA
Indica II	465	33.50%	65.20%	0.65%	0.65%	NA
Indica III	913	76.10%	21.20%	0.11%	2.52%	NA
Indica Intermediate	786	64.20%	29.30%	1.40%	5.09%	NA
Temperate Japonica	767	4.80%	84.60%	0.26%	10.30%	NA
Tropical Japonica	504	7.90%	4.00%	1.39%	86.71%	NA
Japonica Intermediate	241	29.50%	34.40%	0.83%	35.27%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	28.90%	61.10%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0908678620	T -> G	LOC_Os09g14620.1	downstream_gene_variant ; 4341.0bp to feature; MODIFIER	silent_mutation	Average:29.344; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0908678620	T -> G	LOC_Os09g14640.1	downstream_gene_variant ; 4088.0bp to feature; MODIFIER	silent_mutation	Average:29.344; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0908678620	T -> G	LOC_Os09g14630.1	intron_variant ; MODIFIER	silent_mutation	Average:29.344; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0908678620	T -> DEL	N	N	silent_mutation	Average:29.344; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0908678620	3.04E-06	NA	mr1528_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
vg0908678620	NA	5.17E-06	mr1528_2	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