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Detailed information for vg0401663988:

Variant ID: vg0401663988 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1663988
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, C: 0.17, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

AGTCCGCCGCCCCCTACGCTGGCCCTCTCACTTCCAGGTGACGAACTCTGGTTGACGGCGGCTGTGTTTAGTTCACAGTTTGGTTGAAATTGTAACGATG[T/C]
GATGGAAAAGTTGGAAGTTTGTGTGTGTAGAAAAGTTTTGATGTGATAGAATAGTTGGAAGTTTGAAGAATTATTTTGGATCTAAACACGGCCCACATCG

Reverse complement sequence

CGATGTGGGCCGTGTTTAGATCCAAAATAATTCTTCAAACTTCCAACTATTCTATCACATCAAAACTTTTCTACACACACAAACTTCCAACTTTTCCATC[A/G]
CATCGTTACAATTTCAACCAAACTGTGAACTAAACACAGCCGCCGTCAACCAGAGTTCGTCACCTGGAAGTGAGAGGGCCAGCGTAGGGGGCGGCGGACT

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	18.90%	16.20%	0.72%	64.20%	NA
All Indica	2759	17.80%	9.30%	1.01%	71.87%	NA
All Japonica	1512	22.30%	30.80%	0.26%	46.63%	NA
Aus	269	4.50%	7.80%	0.37%	87.36%	NA
Indica I	595	7.60%	21.70%	3.36%	67.39%	NA
Indica II	465	41.50%	6.50%	0.65%	51.40%	NA
Indica III	913	6.70%	2.00%	0.11%	91.24%	NA
Indica Intermediate	786	24.60%	10.10%	0.51%	64.89%	NA
Temperate Japonica	767	30.80%	51.50%	0.52%	17.21%	NA
Tropical Japonica	504	13.10%	7.10%	0.00%	79.76%	NA
Japonica Intermediate	241	14.50%	14.50%	0.00%	70.95%	NA
VI/Aromatic	96	33.30%	2.10%	0.00%	64.58%	NA
Intermediate	90	23.30%	21.10%	1.11%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401663988	T -> C	LOC_Os04g03740-LOC_Os04g03760	intergenic_region ; MODIFIER	silent_mutation	Average:10.5; most accessible tissue: Callus, score: 64.987	N	N	N	N
vg0401663988	T -> DEL	N	N	silent_mutation	Average:10.5; most accessible tissue: Callus, score: 64.987	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401663988	NA	1.45E-09	mr1137	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
vg0401663988	NA	2.13E-07	mr1617	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
vg0401663988	6.68E-07	6.68E-07	mr1335_2	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