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Detailed information for vg0704650193:

Variant ID: vg0704650193 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4650193
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTGTTGGGGACAGATTTAGTGTTGGTGCTTTTAGCTGTCACCACTCTGGTGATACCAACGCTCGTGATTGACTCAAGCTTGATGTTGCGGCATGTCAC[A/G]
AGCATGTTGTTGAGCGTGGCAATAATCTTGGCACACAACTCCTGGAATGTATCCTTTGGTTTCATCTCAACTTGAGCCATGTCGCCCTCGGCTTTGTTGG

Reverse complement sequence

CCAACAAAGCCGAGGGCGACATGGCTCAAGTTGAGATGAAACCAAAGGATACATTCCAGGAGTTGTGTGCCAAGATTATTGCCACGCTCAACAACATGCT[T/C]
GTGACATGCCGCAACATCAAGCTTGAGTCAATCACGAGCGTTGGTATCACCAGAGTGGTGACAGCTAAAAGCACCAACACTAAATCTGTCCCCAACACAT

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	70.50%	29.20%	0.08%	0.21%	NA
All Indica	2759	97.60%	2.10%	0.07%	0.25%	NA
All Japonica	1512	33.80%	66.00%	0.00%	0.20%	NA
Aus	269	25.70%	74.30%	0.00%	0.00%	NA
Indica I	595	99.50%	0.20%	0.00%	0.34%	NA
Indica II	465	97.00%	2.80%	0.22%	0.00%	NA
Indica III	913	98.00%	1.60%	0.11%	0.22%	NA
Indica Intermediate	786	96.10%	3.60%	0.00%	0.38%	NA
Temperate Japonica	767	58.90%	40.90%	0.00%	0.13%	NA
Tropical Japonica	504	4.40%	95.40%	0.00%	0.20%	NA
Japonica Intermediate	241	15.40%	84.20%	0.00%	0.41%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	47.80%	50.00%	2.22%	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
vg0704650193	A -> DEL	LOC_Os07g08940.1	N	frameshift_variant	Average:53.325; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0704650193	A -> G	LOC_Os07g08940.1	synonymous_variant ; p.Leu121Leu; LOW	synonymous_codon	Average:53.325; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0704650193	NA	2.61E-06	mr1057	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
vg0704650193	NA	2.87E-13	mr1552_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