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Detailed information for vg1010744278:

Variant ID: vg1010744278 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10744278
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:

GACATCGAATATGGAAGTGCATGCCGAGATGTCGAAGCTCTTGTAGACGTCGTGGTTGGTGAAGTAGCAAAACTTGCGAAGTAGCGGCAATTAGGTTTGC[C/T]
GGTGCCGAAGATAATATAGATGAAGTCGCTTCACCATGGTGACAAAGTTGCATAGCTGTGATGAAGTGAACACGAGTCGGCGGCAACAGAAGCAAACCGG

Reverse complement sequence

CCGGTTTGCTTCTGTTGCCGCCGACTCGTGTTCACTTCATCACAGCTATGCAACTTTGTCACCATGGTGAAGCGACTTCATCTATATTATCTTCGGCACC[G/A]
GCAAACCTAATTGCCGCTACTTCGCAAGTTTTGCTACTTCACCAACCACGACGTCTACAAGAGCTTCGACATCTCGGCATGCACTTCCATATTCGATGTC

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	37.40%	2.70%	7.74%	52.14%	NA
All Indica	2759	17.00%	4.50%	11.45%	67.05%	NA
All Japonica	1512	78.70%	0.10%	0.79%	20.37%	NA
Aus	269	5.20%	0.00%	6.69%	88.10%	NA
Indica I	595	12.30%	6.90%	18.66%	62.18%	NA
Indica II	465	5.40%	3.70%	8.82%	82.15%	NA
Indica III	913	27.80%	2.60%	7.78%	61.77%	NA
Indica Intermediate	786	14.80%	5.50%	11.83%	67.94%	NA
Temperate Japonica	767	74.30%	0.00%	0.91%	24.77%	NA
Tropical Japonica	504	94.20%	0.00%	0.00%	5.75%	NA
Japonica Intermediate	241	60.20%	0.80%	2.07%	36.93%	NA
VI/Aromatic	96	58.30%	0.00%	14.58%	27.08%	NA
Intermediate	90	44.40%	1.10%	6.67%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1010744278	C -> T	LOC_Os10g21130.1	downstream_gene_variant ; 4615.0bp to feature; MODIFIER	silent_mutation	Average:10.988; most accessible tissue: Minghui63 young leaf, score: 16.99	N	N	N	N
vg1010744278	C -> T	LOC_Os10g21110-LOC_Os10g21130	intergenic_region ; MODIFIER	silent_mutation	Average:10.988; most accessible tissue: Minghui63 young leaf, score: 16.99	N	N	N	N
vg1010744278	C -> DEL	N	N	silent_mutation	Average:10.988; most accessible tissue: Minghui63 young leaf, score: 16.99	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010744278	NA	6.13E-09	mr1342	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
vg1010744278	1.37E-06	NA	mr1502	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
vg1010744278	4.14E-07	NA	mr1502	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
vg1010744278	3.00E-06	NA	mr1519	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
vg1010744278	4.48E-09	NA	mr1798	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
vg1010744278	1.62E-07	6.66E-10	mr1798	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
vg1010744278	8.23E-06	NA	mr1913	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