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Detailed information for vg1001933839:

Variant ID: vg1001933839 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1933839
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, C: 0.13, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

TACAACAAACTCTTTCACTCTACCTCCATCTGAAGTATTTATGTGTTTTTTGTGCAGCTCTCTAAAAAGCTTGCTTCCCATCTCAGAACAGCCACCCTTA[T/C]
ATATAATTAGCTGGAAATGGTTCAGAGCAAAACCAGCAGCCATTTTATCCACAGCTGTTTTCAAGGGATGAGAAAAGTGACTGCAATTTGCCAAGTTTAA

Reverse complement sequence

TTAAACTTGGCAAATTGCAGTCACTTTTCTCATCCCTTGAAAACAGCTGTGGATAAAATGGCTGCTGGTTTTGCTCTGAACCATTTCCAGCTAATTATAT[A/G]
TAAGGGTGGCTGTTCTGAGATGGGAAGCAAGCTTTTTAGAGAGCTGCACAAAAAACACATAAATACTTCAGATGGAGGTAGAGTGAAAGAGTTTGTTGTA

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	47.10%	36.20%	0.49%	16.12%	NA
All Indica	2759	16.50%	59.50%	0.80%	23.20%	NA
All Japonica	1512	96.40%	3.00%	0.00%	0.60%	NA
Aus	269	59.90%	1.50%	0.37%	38.29%	NA
Indica I	595	3.40%	54.60%	1.34%	40.67%	NA
Indica II	465	17.60%	66.70%	0.43%	15.27%	NA
Indica III	913	21.70%	57.70%	0.11%	20.48%	NA
Indica Intermediate	786	19.80%	60.90%	1.40%	17.81%	NA
Temperate Japonica	767	98.60%	0.50%	0.00%	0.91%	NA
Tropical Japonica	504	92.90%	7.10%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.10%	0.00%	0.83%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	67.80%	25.60%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001933839	T -> C	LOC_Os10g04160.1	missense_variant ; p.Tyr15Cys; MODERATE	nonsynonymous_codon ; Y15C	Average:31.45; most accessible tissue: Minghui63 root, score: 66.549	unknown	unknown	TOLERATED	0.09
vg1001933839	T -> DEL	LOC_Os10g04160.1	N	frameshift_variant	Average:31.45; most accessible tissue: Minghui63 root, score: 66.549	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001933839	NA	1.04E-07	mr1486	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
vg1001933839	NA	1.37E-06	mr1486_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