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Detailed information for vg0729424427:

Variant ID: vg0729424427 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29424427
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACAGTCATGTTGGGCTACAGACATATCCCGAGCTCACAACTGCATTACAAAAGGGAAAGCGGAAGCCAAGACTTGGACCATTCATCACAGGCGCGACTT[A/G]
GGAACTAGGCAGAAACCCTAAAACTCATCGTAGCCGACTTGCTCCTGGAAGAACTCCTCATCAGCGGGATCTACTTCATCTTCTTCAGCAACTGGGGAGG

Reverse complement sequence

CCTCCCCAGTTGCTGAAGAAGATGAAGTAGATCCCGCTGATGAGGAGTTCTTCCAGGAGCAAGTCGGCTACGATGAGTTTTAGGGTTTCTGCCTAGTTCC[T/C]
AAGTCGCGCCTGTGATGAATGGTCCAAGTCTTGGCTTCCGCTTTCCCTTTTGTAATGCAGTTGTGAGCTCGGGATATGTCTGTAGCCCAACATGACTGTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.80%	36.20%	0.06%	0.00%	NA
All Indica	2759	94.80%	5.10%	0.11%	0.00%	NA
All Japonica	1512	12.80%	87.20%	0.00%	0.00%	NA
Aus	269	56.90%	43.10%	0.00%	0.00%	NA
Indica I	595	98.30%	1.50%	0.17%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	92.90%	7.10%	0.00%	0.00%	NA
Indica Intermediate	786	92.90%	6.90%	0.25%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	21.60%	78.40%	0.00%	0.00%	NA
Japonica Intermediate	241	32.40%	67.60%	0.00%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	47.80%	52.20%	0.00%	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
vg0729424427	A -> G	LOC_Os07g49130.1	upstream_gene_variant ; 3995.0bp to feature; MODIFIER	silent_mutation	Average:51.458; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0729424427	A -> G	LOC_Os07g49120-LOC_Os07g49130	intergenic_region ; MODIFIER	silent_mutation	Average:51.458; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729424427	NA	1.08E-07	mr1522	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
vg0729424427	8.17E-08	4.87E-09	mr1835	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
vg0729424427	NA	9.76E-06	mr1911_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
vg0729424427	NA	1.67E-07	mr1929_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