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Detailed information for vg0906163068:

Variant ID: vg0906163068 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6163068
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCTTGCCATCAAACTCAAAAGCTGTGCGGGATCTCTCTTTGATTGGAGCTAATCGACTTTTGATGAAGTGCCGAGTGATCTGTTCTCCCTGCAAACCTT[G/A]
TTCCTTCAGTTTTAGCATGCGTTCCATTAATTCCACTGCCTGAGCAGCTTCATCTCCCATAGGCAATGAGTTCCATGTGTCCTGGTAAACCGGAGGAAGA

Reverse complement sequence

TCTTCCTCCGGTTTACCAGGACACATGGAACTCATTGCCTATGGGAGATGAAGCTGCTCAGGCAGTGGAATTAATGGAACGCATGCTAAAACTGAAGGAA[C/T]
AAGGTTTGCAGGGAGAACAGATCACTCGGCACTTCATCAAAAGTCGATTAGCTCCAATCAAAGAGAGATCCCGCACAGCTTTTGAGTTTGATGGCAAGCA

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	89.10%	4.20%	1.78%	4.95%	NA
All Indica	2759	93.30%	4.90%	1.27%	0.51%	NA
All Japonica	1512	82.10%	3.50%	1.98%	12.37%	NA
Aus	269	91.10%	0.40%	2.23%	6.32%	NA
Indica I	595	88.40%	10.90%	0.67%	0.00%	NA
Indica II	465	97.80%	0.20%	1.51%	0.43%	NA
Indica III	913	94.00%	3.50%	2.19%	0.33%	NA
Indica Intermediate	786	93.60%	4.70%	0.51%	1.15%	NA
Temperate Japonica	767	91.10%	0.40%	0.78%	7.69%	NA
Tropical Japonica	504	78.80%	8.30%	1.79%	11.11%	NA
Japonica Intermediate	241	60.60%	3.30%	6.22%	29.88%	NA
VI/Aromatic	96	66.70%	7.30%	10.42%	15.62%	NA
Intermediate	90	92.20%	3.30%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906163068	G -> DEL	LOC_Os09g11110.1	N	frameshift_variant	Average:11.083; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg0906163068	G -> A	LOC_Os09g11110.1	stop_gained ; p.Gln101*; HIGH	stop_gained	Average:11.083; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906163068	NA	5.49E-06	mr1471_2	Ind_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