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Detailed information for vg1004977357:

Variant ID: vg1004977357 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4977357
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, T: 0.36, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

ACGATGATTCAGACCGAACTGGCAACCCGACCCAGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTTGTTAAGCAGGTTTT[T/A]
AGAATTAAAACACTAACTTGGGTACATTGCTCGGCTTGTCCATAACCGAGGGCGCGGCTATTCGAATAGATTATACTCTGATCAGAGGTGTATATCTTTA

Reverse complement sequence

TAAAGATATACACCTCTGATCAGAGTATAATCTATTCGAATAGCCGCGCCCTCGGTTATGGACAAGCCGAGCAATGTACCCAAGTTAGTGTTTTAATTCT[A/T]
AAAACCTGCTTAACAACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCTGGGTCGGGTTGCCAGTTCGGTCTGAATCATCGT

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	21.50%	18.20%	37.33%	23.00%	NA
All Indica	2759	3.00%	22.90%	52.41%	21.67%	NA
All Japonica	1512	58.00%	0.40%	11.90%	29.70%	NA
Aus	269	0.70%	75.80%	18.22%	5.20%	NA
Indica I	595	2.00%	21.50%	54.29%	22.18%	NA
Indica II	465	2.80%	10.80%	57.42%	29.03%	NA
Indica III	913	3.20%	34.30%	47.10%	15.44%	NA
Indica Intermediate	786	3.70%	17.90%	54.20%	24.17%	NA
Temperate Japonica	767	65.30%	0.00%	7.69%	26.99%	NA
Tropical Japonica	504	51.20%	0.80%	13.29%	34.72%	NA
Japonica Intermediate	241	49.00%	0.80%	22.41%	27.80%	NA
VI/Aromatic	96	26.00%	8.30%	62.50%	3.12%	NA
Intermediate	90	33.30%	8.90%	32.22%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004977357	T -> A	LOC_Os10g09220.1	downstream_gene_variant ; 2547.0bp to feature; MODIFIER	silent_mutation	Average:25.565; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg1004977357	T -> A	LOC_Os10g09210.1	intron_variant ; MODIFIER	silent_mutation	Average:25.565; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg1004977357	T -> DEL	N	N	silent_mutation	Average:25.565; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004977357	NA	5.48E-07	mr1278	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
vg1004977357	NA	3.35E-07	mr1768	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
vg1004977357	NA	7.90E-06	mr1835	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
vg1004977357	1.05E-06	1.04E-06	mr1869	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
vg1004977357	NA	3.27E-06	mr1768_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