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Detailed information for vg1001020266:

Variant ID: vg1001020266 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1020266
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TCCAAGTCTATTTCTCCGATATGCATTCCCTCTTCTGTAAGTGCTAGACTTGAACGTGTTAATAAATCACTATACCTATATGCGTAGCTCATTTGATCAT[C/T]
CATTGTTGGCAGGATGAATTACATGGAAGCCGAAGCGATGAGAAAGCCTGTCGGCTACCTAAACTCGTGCAGGATAAGTCAGCCGAACCACACATACACG

Reverse complement sequence

CGTGTATGTGTGGTTCGGCTGACTTATCCTGCACGAGTTTAGGTAGCCGACAGGCTTTCTCATCGCTTCGGCTTCCATGTAATTCATCCTGCCAACAATG[G/A]
ATGATCAAATGAGCTACGCATATAGGTATAGTGATTTATTAACACGTTCAAGTCTAGCACTTACAGAAGAGGGAATGCATATCGGAGAAATAGACTTGGA

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	80.40%	15.80%	1.12%	2.69%	NA
All Indica	2759	99.10%	0.80%	0.04%	0.04%	NA
All Japonica	1512	47.90%	40.70%	3.11%	8.27%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.60%	0.30%	0.00%	0.11%	NA
Indica Intermediate	786	97.60%	2.30%	0.13%	0.00%	NA
Temperate Japonica	767	73.80%	21.60%	1.30%	3.26%	NA
Tropical Japonica	504	21.80%	62.90%	3.37%	11.90%	NA
Japonica Intermediate	241	19.90%	55.20%	8.30%	16.60%	NA
VI/Aromatic	96	14.60%	84.40%	1.04%	0.00%	NA
Intermediate	90	66.70%	27.80%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001020266	C -> T	LOC_Os10g02644.1	downstream_gene_variant ; 3181.0bp to feature; MODIFIER	silent_mutation	Average:63.973; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg1001020266	C -> T	LOC_Os10g02640.1	intron_variant ; MODIFIER	silent_mutation	Average:63.973; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N
vg1001020266	C -> DEL	N	N	silent_mutation	Average:63.973; most accessible tissue: Zhenshan97 panicle, score: 87.126	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001020266	NA	5.36E-10	mr1128	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
vg1001020266	8.82E-11	NA	mr1300	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
vg1001020266	5.73E-07	1.81E-10	mr1300	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
vg1001020266	4.55E-09	NA	mr1310	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
vg1001020266	7.43E-06	3.36E-11	mr1310	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
vg1001020266	NA	3.98E-14	mr1330	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
vg1001020266	NA	1.38E-10	mr1332	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
vg1001020266	NA	4.06E-10	mr1336	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
vg1001020266	NA	5.08E-08	mr1338	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
vg1001020266	NA	5.16E-08	mr1514	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
vg1001020266	NA	1.23E-12	mr1521	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
vg1001020266	NA	2.27E-13	mr1579	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
vg1001020266	NA	2.82E-20	mr1580	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
vg1001020266	NA	1.29E-15	mr1701	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
vg1001020266	NA	4.55E-09	mr1779	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
vg1001020266	1.02E-12	NA	mr1926	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
vg1001020266	9.72E-08	5.03E-14	mr1926	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
vg1001020266	NA	5.77E-07	mr1959	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
vg1001020266	4.68E-10	NA	mr1310_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
vg1001020266	NA	4.57E-12	mr1310_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
vg1001020266	9.19E-06	NA	mr1959_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
vg1001020266	NA	8.30E-09	mr1959_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