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Detailed information for vg0729064560:

Variant ID: vg0729064560 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29064560
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATATGAGATGTGACATATTCTACGAGAAACGCTCAGGGGTCTTCCGGCTAGCTCCACTGGATGGTGGGCTAGCCGGCCTGGGTTTGAAGTCTCTCATC[T/C]
ATTCTATTTATTTGATATTAGATCTTTTAATATTTGTGTTTTTTTAATTCTAGTACTACGAATTTAAATAGAGTTGTATCGGTGATATAGGCCCAGGGAT

Reverse complement sequence

ATCCCTGGGCCTATATCACCGATACAACTCTATTTAAATTCGTAGTACTAGAATTAAAAAAACACAAATATTAAAAGATCTAATATCAAATAAATAGAAT[A/G]
GATGAGAGACTTCAAACCCAGGCCGGCTAGCCCACCATCCAGTGGAGCTAGCCGGAAGACCCCTGAGCGTTTCTCGTAGAATATGTCACATCTCATATTA

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	78.40%	21.30%	0.32%	0.00%	NA
All Indica	2759	98.90%	1.00%	0.07%	0.00%	NA
All Japonica	1512	38.10%	61.20%	0.73%	0.00%	NA
Aus	269	88.50%	11.50%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.60%	0.13%	0.00%	NA
Temperate Japonica	767	8.70%	90.20%	1.04%	0.00%	NA
Tropical Japonica	504	84.10%	15.90%	0.00%	0.00%	NA
Japonica Intermediate	241	35.30%	63.50%	1.24%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	25.60%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0729064560	T -> C	LOC_Os07g48550-LOC_Os07g48560	intergenic_region ; MODIFIER	silent_mutation	Average:61.944; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729064560	NA	8.47E-08	mr1552	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
vg0729064560	NA	6.39E-24	mr1862	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
vg0729064560	NA	2.20E-39	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
vg0729064560	NA	4.66E-06	mr1174_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
vg0729064560	NA	4.09E-09	mr1304_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
vg0729064560	NA	7.59E-07	mr1347_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
vg0729064560	NA	3.49E-06	mr1386_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
vg0729064560	NA	1.82E-09	mr1551_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
vg0729064560	1.33E-08	NA	mr1679_2	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
vg0729064560	2.21E-06	NA	mr1679_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
vg0729064560	4.12E-06	NA	mr1720_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
vg0729064560	4.66E-06	NA	mr1720_2	Jap_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
vg0729064560	NA	2.25E-07	mr1905_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