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Detailed information for vg0906540051:

Variant ID: vg0906540051 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6540051
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.21, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

ACAAGCGCTCGAATGCTGTCACCCGCTTTCTCTTGTTGTTGCGCTTCTGAGATGGGGTTGAGGTTGGCTTCTTCTTAGGCTCACCGTCGCCAAGCTGGAA[T/C]
TGCTCCTTCACCTTGGGCGCCTTGGGCGTGGCCTTTTGGGGTGAAGGACGATTATTGCAGGGTGCGAGCTATGGCTACGATTGCGAGGGTTTGGCTTGGG

Reverse complement sequence

CCCAAGCCAAACCCTCGCAATCGTAGCCATAGCTCGCACCCTGCAATAATCGTCCTTCACCCCAAAAGGCCACGCCCAAGGCGCCCAAGGTGAAGGAGCA[A/G]
TTCCAGCTTGGCGACGGTGAGCCTAAGAAGAAGCCAACCTCAACCCCATCTCAGAAGCGCAACAACAAGAGAAAGCGGGTGACAGCATTCGAGCGCTTGT

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	39.00%	31.70%	1.69%	27.59%	NA
All Indica	2759	16.90%	35.40%	2.79%	44.91%	NA
All Japonica	1512	86.00%	13.00%	0.00%	0.99%	NA
Aus	269	7.80%	78.80%	0.00%	13.38%	NA
Indica I	595	27.70%	6.10%	3.70%	62.52%	NA
Indica II	465	7.70%	56.80%	1.29%	34.19%	NA
Indica III	913	13.30%	38.20%	2.63%	45.89%	NA
Indica Intermediate	786	18.20%	41.90%	3.18%	36.77%	NA
Temperate Japonica	767	96.30%	3.40%	0.00%	0.26%	NA
Tropical Japonica	504	84.10%	13.30%	0.00%	2.58%	NA
Japonica Intermediate	241	57.30%	42.70%	0.00%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	45.60%	35.60%	3.33%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906540051	T -> DEL	LOC_Os09g11720.1	N	frameshift_variant	Average:43.096; most accessible tissue: Minghui63 young leaf, score: 86.378	N	N	N	N
vg0906540051	T -> C	LOC_Os09g11720.1	missense_variant ; p.Ile76Thr; MODERATE	nonsynonymous_codon ; I76A	Average:43.096; most accessible tissue: Minghui63 young leaf, score: 86.378	unknown	unknown	TOLERATED	0.11
vg0906540051	T -> C	LOC_Os09g11720.1	missense_variant ; p.Ile76Thr; MODERATE	nonsynonymous_codon ; I76T	Average:43.096; most accessible tissue: Minghui63 young leaf, score: 86.378	unknown	unknown	TOLERATED	0.34

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906540051	NA	5.38E-20	mr1557	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
vg0906540051	NA	3.67E-09	mr1557	Ind_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
vg0906540051	4.08E-06	8.20E-07	mr1098_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
vg0906540051	NA	5.97E-06	mr1114_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
vg0906540051	NA	8.05E-06	mr1150_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
vg0906540051	NA	2.97E-09	mr1232_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
vg0906540051	NA	1.77E-06	mr1240_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