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Detailed information for vg0801634534:

Variant ID: vg0801634534 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1634534
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTATATAAATTCCTCCATGGTCATCAGCTCGATCGGTCACTCTCAGCAAGCTCGATCAGATTCAGAGATGGCATCGTCTCGCCCCATCTCGGAGAGCA[C/T]
CATCACGAGGTCGACGTGCGCGACGCGGACGGCGCGCGCCACGCACCAGTTCGAGATCGTCGGGTACAGCCTCAAGAGGTGCCTCGCCGCCGGCGAGTTC

Reverse complement sequence

GAACTCGCCGGCGGCGAGGCACCTCTTGAGGCTGTACCCGACGATCTCGAACTGGTGCGTGGCGCGCGCCGTCCGCGTCGCGCACGTCGACCTCGTGATG[G/A]
TGCTCTCCGAGATGGGGCGAGACGATGCCATCTCTGAATCTGATCGAGCTTGCTGAGAGTGACCGATCGAGCTGATGACCATGGAGGAATTTATATACTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.60%	28.50%	0.19%	0.72%	NA
All Indica	2759	51.80%	46.60%	0.33%	1.23%	NA
All Japonica	1512	98.00%	2.00%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	31.60%	65.70%	0.34%	2.35%	NA
Indica II	465	21.10%	78.90%	0.00%	0.00%	NA
Indica III	913	83.80%	15.30%	0.11%	0.77%	NA
Indica Intermediate	786	48.10%	49.50%	0.76%	1.65%	NA
Temperate Japonica	767	97.00%	3.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	73.30%	26.70%	0.00%	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
vg0801634534	C -> T	LOC_Os08g03490.1	missense_variant ; p.Thr11Ile; MODERATE	nonsynonymous_codon ; T11I	Average:71.41; most accessible tissue: Minghui63 root, score: 77.29	unknown	unknown	TOLERATED	0.23
vg0801634534	C -> DEL	LOC_Os08g03490.1	N	frameshift_variant	Average:71.41; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801634534	NA	3.69E-08	mr1739	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
vg0801634534	8.11E-06	6.91E-14	mr1739	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
vg0801634534	NA	1.28E-11	mr1751	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
vg0801634534	NA	1.08E-11	mr1734_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
vg0801634534	NA	1.27E-11	mr1739_2	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