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Detailed information for vg0609473231:

Variant ID: vg0609473231 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9473231
Reference Allele: G	Alternative Allele: A,C
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGGCATCTGACAATCTTCCACCAACTTACTAAACTTCTCAAAATCTCTGTCGTTGTCCTCTGCGTCTTCAATGTTATGCAACATTGTAGATAGACATT[G/A,C]
AGTGTCCAAATCTATGGTATCTCCACCTAACGGAGAAGGTACGAACATGCCTTCTCGAGCTGCGGCGGTGTTCTCTACATCCTGATCCAACACTTCTTCA

Reverse complement sequence

TGAAGAAGTGTTGGATCAGGATGTAGAGAACACCGCCGCAGCTCGAGAAGGCATGTTCGTACCTTCTCCGTTAGGTGGAGATACCATAGATTTGGACACT[C/T,G]
AATGTCTATCTACAATGTTGCATAACATTGAAGACGCAGAGGACAACGACAGAGATTTTGAGAAGTTTAGTAAGTTGGTGGAAGATTGTCAGATGCCCTT

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	68.80%	19.70%	10.88%	0.66%	NA
All Indica	2759	94.20%	2.50%	3.37%	0.00%	NA
All Japonica	1512	33.50%	43.70%	20.77%	2.05%	NA
Aus	269	23.00%	45.40%	31.60%	0.00%	NA
Indica I	595	91.40%	2.00%	6.55%	0.00%	NA
Indica II	465	96.60%	0.40%	3.01%	0.00%	NA
Indica III	913	95.00%	3.90%	1.10%	0.00%	NA
Indica Intermediate	786	93.90%	2.30%	3.82%	0.00%	NA
Temperate Japonica	767	52.90%	21.40%	21.90%	3.78%	NA
Tropical Japonica	504	12.90%	72.00%	15.08%	0.00%	NA
Japonica Intermediate	241	14.50%	55.60%	29.05%	0.83%	NA
VI/Aromatic	96	21.90%	62.50%	15.62%	0.00%	NA
Intermediate	90	71.10%	21.10%	7.78%	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
vg0609473231	G -> C	LOC_Os06g16510.1	missense_variant ; p.Gln71Glu; MODERATE	N	Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0609473231	G -> A	LOC_Os06g16510.1	stop_gained ; p.Gln71*; HIGH	stop_gained	Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0609473231	G -> DEL	LOC_Os06g16510.1	N	frameshift_variant	Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609473231	NA	2.46E-09	mr1666	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
vg0609473231	NA	3.04E-07	mr1570_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