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Detailed information for vg0723567969:

Variant ID: vg0723567969 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 23567969
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATGGCTCAACTCATTGGTGATGATTACTCTGCTTATTTAACAACTGTTAGGGCTTCATTGTCTGATACTTTTGCTAAGTATGAAAGAAAGTTTGGTT[C/A]
TGTTGGATTGCGTAGTTCCACTATTCTAGGCCCTTCCACTAGTAAGAAAAGGACTGCATGGGGGAAGATTTTTGGTTCTGGTAATGCAGGTGCCAGTCTA

Reverse complement sequence

TAGACTGGCACCTGCATTACCAGAACCAAAAATCTTCCCCCATGCAGTCCTTTTCTTACTAGTGGAAGGGCCTAGAATAGTGGAACTACGCAATCCAACA[G/T]
AACCAAACTTTCTTTCATACTTAGCAAAAGTATCAGACAATGAAGCCCTAACAGTTGTTAAATAAGCAGAGTAATCATCACCAATGAGTTGAGCCATAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.10%	3.90%	0.02%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	44.20%	55.40%	0.37%	0.00%	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	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	96.70%	3.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0723567969	C -> A	LOC_Os07g39340.1	missense_variant ; p.Ser442Tyr; MODERATE	nonsynonymous_codon ; S442Y	Average:49.641; most accessible tissue: Minghui63 panicle, score: 76.913	unknown	unknown	TOLERATED	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0723567969	NA	2.24E-17	mr1587_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
vg0723567969	4.26E-06	NA	mr1865_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