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Detailed information for vg0701530964:

Variant ID: vg0701530964 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 1530964
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGAGGGGGAGGAGTCGACGAAGGGATTAAAAATGAGAATTGGTATTTTTGGAAACGGGAATAAGTATTTGGCGAGGATTCAAAAGGAGGCGATTGACGT[T/C]
TGGAATAATTGAATCAGAATTGGAAATCTTGAGGTGGAGGATTTTGATTTTGATGAGAGAGAACAACGGGATTTGAATTGAGATCCACGGCACGACTTAG

Reverse complement sequence

CTAAGTCGTGCCGTGGATCTCAATTCAAATCCCGTTGTTCTCTCTCATCAAAATCAAAATCCTCCACCTCAAGATTTCCAATTCTGATTCAATTATTCCA[A/G]
ACGTCAATCGCCTCCTTTTGAATCCTCGCCAAATACTTATTCCCGTTTCCAAAAATACCAATTCTCATTTTTAATCCCTTCGTCGACTCCTCCCCCTCAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.10%	0.70%	4.68%	33.56%	NA
All Indica	2759	35.60%	1.00%	7.87%	55.53%	NA
All Japonica	1512	99.50%	0.00%	0.00%	0.46%	NA
Aus	269	88.10%	0.40%	1.12%	10.41%	NA
Indica I	595	33.80%	0.00%	6.72%	59.50%	NA
Indica II	465	63.20%	0.40%	4.30%	32.04%	NA
Indica III	913	21.20%	1.90%	9.64%	67.25%	NA
Indica Intermediate	786	37.30%	1.10%	8.78%	52.80%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	1.00%	1.04%	3.12%	NA
Intermediate	90	81.10%	1.10%	0.00%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0701530964	T -> DEL	N	N	silent_mutation	Average:54.963; most accessible tissue: Minghui63 flag leaf, score: 84.791	N	N	N	N
vg0701530964	T -> C	LOC_Os07g03740.1	intron_variant ; MODIFIER	silent_mutation	Average:54.963; most accessible tissue: Minghui63 flag leaf, score: 84.791	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0701530964	NA	1.32E-06	mr1031	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
vg0701530964	NA	6.89E-07	mr1056	Ind_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
vg0701530964	NA	1.10E-06	mr1796	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