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Detailed information for vg1004352698:

Variant ID: vg1004352698 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4352698
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTACTACTCTCCTAGCAACTTTAGATTGATCATTATCTAAGTAATACTCCATCTGTTTTTCGGCGATATAATATTTGAGCGCTTGCCGCCGAATCTTT[C/T]
GATCAACCTTAAGTGTAGGATCATTCAAATATCTAATCAAATGAATTCTCCAAGCTACCTCTAACTCATGGGCACAAATGTCCGAATTCACAATTAAGTC

Reverse complement sequence

GACTTAATTGTGAATTCGGACATTTGTGCCCATGAGTTAGAGGTAGCTTGGAGAATTCATTTGATTAGATATTTGAATGATCCTACACTTAAGGTTGATC[G/A]
AAAGATTCGGCGGCAAGCGCTCAAATATTATATCGCCGAAAAACAGATGGAGTATTACTTAGATAATGATCAATCTAAAGTTGCTAGGAGAGTAGTACAT

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	26.70%	16.40%	18.09%	38.83%	NA
All Indica	2759	11.90%	16.20%	29.03%	42.84%	NA
All Japonica	1512	57.10%	1.10%	1.72%	40.08%	NA
Aus	269	4.10%	93.30%	0.00%	2.60%	NA
Indica I	595	1.30%	41.80%	15.80%	41.01%	NA
Indica II	465	14.80%	10.80%	26.45%	47.96%	NA
Indica III	913	19.10%	3.40%	33.08%	44.47%	NA
Indica Intermediate	786	9.90%	14.90%	35.88%	39.31%	NA
Temperate Japonica	767	82.70%	0.10%	0.78%	16.43%	NA
Tropical Japonica	504	17.10%	2.00%	2.18%	78.77%	NA
Japonica Intermediate	241	59.80%	2.10%	3.73%	34.44%	NA
VI/Aromatic	96	35.40%	39.60%	12.50%	12.50%	NA
Intermediate	90	25.60%	25.60%	17.78%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004352698	C -> T	LOC_Os10g08030.1	missense_variant ; p.Arg606Gln; MODERATE	nonsynonymous_codon ; R606Q	Average:33.449; most accessible tissue: Minghui63 panicle, score: 50.413	unknown	unknown	TOLERATED	0.16
vg1004352698	C -> DEL	LOC_Os10g08030.1	N	frameshift_variant	Average:33.449; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004352698	1.67E-06	3.47E-15	mr1853	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