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Detailed information for vg0906481626:

Variant ID: vg0906481626 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6481626
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGTTCTTGTGGGTGTGGTGAGGCCAAAACTAGTGGAGTAGTAAGAAGTTTCTTGAAATCTTCAAAGGCTTTCTGTGCTTCAGGTCCCCACTGGAAATTG[T/C]
CTGTTTTCTTTAACAGTTTGAAGAAGGGCATCCCCCGCTCGCCGAGTCGTGAGACAAACCGGCTGAGCGCCGCCATGCATCCAGTCAGCTTTTGAACGTC

Reverse complement sequence

GACGTTCAAAAGCTGACTGGATGCATGGCGGCGCTCAGCCGGTTTGTCTCACGACTCGGCGAGCGGGGGATGCCCTTCTTCAAACTGTTAAAGAAAACAG[A/G]
CAATTTCCAGTGGGGACCTGAAGCACAGAAAGCCTTTGAAGATTTCAAGAAACTTCTTACTACTCCACTAGTTTTGGCCTCACCACACCCACAAGAACCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.80%	19.70%	11.34%	1.18%	NA
All Indica	2759	54.10%	28.70%	15.19%	2.03%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.00%	NA
Aus	269	36.10%	39.00%	24.91%	0.00%	NA
Indica I	595	62.70%	10.40%	19.33%	7.56%	NA
Indica II	465	61.90%	27.10%	10.97%	0.00%	NA
Indica III	913	41.50%	44.80%	13.58%	0.11%	NA
Indica Intermediate	786	57.50%	24.80%	16.41%	1.27%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	35.40%	21.90%	42.71%	0.00%	NA
Intermediate	90	81.10%	11.10%	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
vg0906481626	T -> DEL	LOC_Os09g11610.1	N	frameshift_variant	Average:35.381; most accessible tissue: Minghui63 flag leaf, score: 74.955	N	N	N	N
vg0906481626	T -> C	LOC_Os09g11610.1	missense_variant ; p.Asp694Gly; MODERATE	nonsynonymous_codon ; D694G	Average:35.381; most accessible tissue: Minghui63 flag leaf, score: 74.955	possibly damaging	1.602	TOLERATED	0.33

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906481626	2.81E-06	NA	mr1607	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