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Detailed information for vg1005678285:

Variant ID: vg1005678285 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5678285
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, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTGTCATATCCCGTACTAGTTTGTTTTTTATAGGACGGAGGGAGTAAATGATATGTCTCTAGACTGGCGTAGCGTATCCATTTGTTTTGCTGCAAGAG[C/T]
AATACAGTTGTTTAGGTATTGGGTTCTAAGCCGCACATAGGCTGGCTCTTGAACTCCTGTTAGAACTTTATTGGCAAATTTCAGGAGGAGAGCAGTGCGC

Reverse complement sequence

GCGCACTGCTCTCCTCCTGAAATTTGCCAATAAAGTTCTAACAGGAGTTCAAGAGCCAGCCTATGTGCGGCTTAGAACCCAATACCTAAACAACTGTATT[G/A]
CTCTTGCAGCAAAACAAATGGATACGCTACGCCAGTCTAGAGACATATCATTTACTCCCTCCGTCCTATAAAAAACAAACTAGTACGGGATATGACACAT

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	95.70%	3.40%	0.15%	0.66%	NA
All Indica	2759	99.50%	0.50%	0.00%	0.07%	NA
All Japonica	1512	92.50%	7.00%	0.13%	0.40%	NA
Aus	269	98.50%	0.00%	0.00%	1.49%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.00%	0.90%	0.00%	0.11%	NA
Indica Intermediate	786	99.40%	0.50%	0.00%	0.13%	NA
Temperate Japonica	767	87.00%	12.90%	0.13%	0.00%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	95.90%	2.10%	0.41%	1.66%	NA
VI/Aromatic	96	39.60%	39.60%	4.17%	16.67%	NA
Intermediate	90	88.90%	6.70%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005678285	C -> T	LOC_Os10g10334.1	intron_variant ; MODIFIER	silent_mutation	Average:44.955; most accessible tissue: Callus, score: 70.863	N	N	N	N
vg1005678285	C -> DEL	N	N	silent_mutation	Average:44.955; most accessible tissue: Callus, score: 70.863	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005678285	2.32E-10	NA	mr1210	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
vg1005678285	8.86E-06	4.39E-09	mr1210	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
vg1005678285	7.43E-11	NA	mr1305	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
vg1005678285	5.82E-06	4.45E-09	mr1305	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
vg1005678285	2.30E-06	3.43E-11	mr1585	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
vg1005678285	5.33E-06	6.49E-11	mr1585	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
vg1005678285	1.58E-10	NA	mr1586	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
vg1005678285	NA	4.22E-08	mr1586	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
vg1005678285	4.45E-06	NA	mr1649	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
vg1005678285	NA	7.03E-06	mr1765	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
vg1005678285	NA	1.42E-07	mr1915	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
vg1005678285	2.99E-08	NA	mr1305_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
vg1005678285	1.33E-06	3.78E-09	mr1305_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
vg1005678285	1.02E-06	2.09E-11	mr1585_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
vg1005678285	2.37E-07	9.29E-12	mr1585_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