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Detailed information for vg0141120189:

Variant ID: vg0141120189 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41120189
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

TCCAGTGTTTGGTCGAACACAATACCTTTTAGGTGATGTTGTTTTAACCTAACAAATTTGAAGGGCAATATCAGACATAGTCCTATTAGATGCTCAAACG[G/A]
CAAAAATTATCATCCTTTGATTGAGCATAAAAGCGATTAAAGAATACATAATATTCAGAAAACAAAATATCTAAGTTTAGTGTCATCAGAAATGGCATTT

Reverse complement sequence

AAATGCCATTTCTGATGACACTAAACTTAGATATTTTGTTTTCTGAATATTATGTATTCTTTAATCGCTTTTATGCTCAATCAAAGGATGATAATTTTTG[C/T]
CGTTTGAGCATCTAATAGGACTATGTCTGATATTGCCCTTCAAATTTGTTAGGTTAAAACAACATCACCTAAAAGGTATTGTGTTCGACCAAACACTGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.60%	40.20%	0.23%	0.00%	NA
All Indica	2759	39.80%	59.80%	0.40%	0.00%	NA
All Japonica	1512	97.20%	2.80%	0.00%	0.00%	NA
Aus	269	34.20%	65.80%	0.00%	0.00%	NA
Indica I	595	52.10%	47.90%	0.00%	0.00%	NA
Indica II	465	25.60%	74.00%	0.43%	0.00%	NA
Indica III	913	33.40%	66.50%	0.11%	0.00%	NA
Indica Intermediate	786	46.20%	52.80%	1.02%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	94.80%	5.20%	0.00%	0.00%	NA
Japonica Intermediate	241	94.20%	5.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	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
vg0141120189	G -> A	LOC_Os01g71050.1	intron_variant ; MODIFIER	silent_mutation	Average:42.942; most accessible tissue: Callus, score: 76.16	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141120189	1.07E-06	NA	mr1748_2	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
vg0141120189	NA	2.66E-06	mr1974_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