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Detailed information for vg0605603220:

Variant ID: vg0605603220 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5603220
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GCCATCACTGTACCTTGCACTAACACCACTAAAGAGTCTGGACTTTGTGGTACTTGTGAGTTGTCAGTCACTTCTACACACTCTACACACTGACAATTCT[T/G]
CGTCCGTATATACCCATAAGACCCTTTTTTTTTAAAAAAAAAGAAAAACTCATATAGGCTTTTTTGGTGAAAATGGTGATGATCTAGCTAGGTTGGTTGG

Reverse complement sequence

CCAACCAACCTAGCTAGATCATCACCATTTTCACCAAAAAAGCCTATATGAGTTTTTCTTTTTTTTTAAAAAAAAAGGGTCTTATGGGTATATACGGACG[A/C]
AGAATTGTCAGTGTGTAGAGTGTGTAGAAGTGACTGACAACTCACAAGTACCACAAAGTCCAGACTCTTTAGTGGTGTTAGTGCAAGGTACAGTGATGGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.50%	48.70%	0.83%	0.00%	NA
All Indica	2759	58.80%	41.10%	0.14%	0.00%	NA
All Japonica	1512	46.50%	51.70%	1.85%	0.00%	NA
Aus	269	3.00%	96.30%	0.74%	0.00%	NA
Indica I	595	89.60%	10.30%	0.17%	0.00%	NA
Indica II	465	36.60%	63.40%	0.00%	0.00%	NA
Indica III	913	50.70%	49.10%	0.22%	0.00%	NA
Indica Intermediate	786	58.00%	41.90%	0.13%	0.00%	NA
Temperate Japonica	767	73.90%	23.50%	2.61%	0.00%	NA
Tropical Japonica	504	9.90%	89.70%	0.40%	0.00%	NA
Japonica Intermediate	241	35.70%	61.80%	2.49%	0.00%	NA
VI/Aromatic	96	16.70%	82.30%	1.04%	0.00%	NA
Intermediate	90	42.20%	53.30%	4.44%	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
vg0605603220	T -> G	LOC_Os06g10730.1	intron_variant ; MODIFIER	silent_mutation	Average:59.404; most accessible tissue: Callus, score: 84.791	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605603220	NA	1.02E-08	mr1087	Jap_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
vg0605603220	NA	5.43E-06	mr1094	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
vg0605603220	NA	2.61E-06	mr1096	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
vg0605603220	NA	1.25E-06	mr1570	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
vg0605603220	NA	9.38E-10	mr1087_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
vg0605603220	NA	2.22E-06	mr1762_2	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