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Detailed information for vg0819413174:

Variant ID: vg0819413174 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19413174
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTCTTCTTTCTTCTAAATGCGTGATGTAGCGGGAGCCACCTCCGATGACCCATGTATACCATCTTTCGTGATTTCTTCAGCCACCGGCTTCGTGTATA[T/A]
TCCTTGCAATCGGAGCATGCATTCTTTCCTTTTATAGTTTGTCCGGAAAGATTACCGAGTGCAGGGTAGTCATTAATAGTGCAGAACAATAGAACTCTTA

Reverse complement sequence

TAAGAGTTCTATTGTTCTGCACTATTAATGACTACCCTGCACTCGGTAATCTTTCCGGACAAACTATAAAAGGAAAGAATGCATGCTCCGATTGCAAGGA[A/T]
TATACACGAAGCCGGTGGCTGAAGAAATCACGAAAGATGGTATACATGGGTCATCGGAGGTGGCTCCCGCTACATCACGCATTTAGAAGAAAGAAGAAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.60%	0.10%	46.76%	9.56%	NA
All Indica	2759	16.70%	0.10%	67.23%	15.95%	NA
All Japonica	1512	83.10%	0.00%	16.47%	0.46%	NA
Aus	269	74.00%	0.40%	25.65%	0.00%	NA
Indica I	595	22.90%	0.20%	47.23%	29.75%	NA
Indica II	465	9.70%	0.20%	64.09%	26.02%	NA
Indica III	913	14.30%	0.00%	82.15%	3.50%	NA
Indica Intermediate	786	19.00%	0.10%	66.92%	13.99%	NA
Temperate Japonica	767	99.50%	0.00%	0.39%	0.13%	NA
Tropical Japonica	504	56.00%	0.00%	43.25%	0.79%	NA
Japonica Intermediate	241	87.60%	0.00%	11.62%	0.83%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	55.60%	0.00%	38.89%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819413174	T -> A	LOC_Os08g31400.1	missense_variant ; p.Glu374Asp; MODERATE	nonsynonymous_codon ; E374D	Average:19.099; most accessible tissue: Minghui63 young leaf, score: 33.985	benign	1.274	TOLERATED	0.81
vg0819413174	T -> DEL	LOC_Os08g31400.1	N	frameshift_variant	Average:19.099; most accessible tissue: Minghui63 young leaf, score: 33.985	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819413174	4.38E-06	7.78E-07	mr1197	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
vg0819413174	6.60E-06	6.60E-06	mr1197	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