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Detailed information for vg0103031868:

Variant ID: vg0103031868 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3031868
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTCGGAGTTTGCCCCACCGTGACCCTCGAGGAGGCCCGCTGCGAGATCTCGCGGGGCGCCGCTCGCCACGCGATGGCCGACCACGTCTTCGTTCGCTAC[G/A]
TCGAGCTCCTCGGCATCCAGCACGAGCCGCCGTGCACCAGCAGGGACACCCACCACCGGGAGGCCATCCGCTTCACCGCCATGGCCCTGGAGAAGGTCAG

Reverse complement sequence

CTGACCTTCTCCAGGGCCATGGCGGTGAAGCGGATGGCCTCCCGGTGGTGGGTGTCCCTGCTGGTGCACGGCGGCTCGTGCTGGATGCCGAGGAGCTCGA[C/T]
GTAGCGAACGAAGACGTGGTCGGCCATCGCGTGGCGAGCGGCGCCCCGCGAGATCTCGCAGCGGGCCTCCTCGAGGGTCACGGTGGGGCAAACTCCGACG

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	74.30%	25.50%	0.08%	0.11%	NA
All Indica	2759	98.30%	1.60%	0.07%	0.07%	NA
All Japonica	1512	28.40%	71.40%	0.07%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	1.50%	0.00%	0.00%	NA
Indica II	465	97.20%	2.20%	0.43%	0.22%	NA
Indica III	913	98.80%	1.10%	0.00%	0.11%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	35.70%	64.30%	0.00%	0.00%	NA
Tropical Japonica	504	12.70%	87.10%	0.00%	0.20%	NA
Japonica Intermediate	241	38.20%	61.40%	0.41%	0.00%	NA
VI/Aromatic	96	41.70%	58.30%	0.00%	0.00%	NA
Intermediate	90	67.80%	28.90%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103031868	G -> A	LOC_Os01g06400.1	missense_variant ; p.Val97Ile; MODERATE	nonsynonymous_codon ; V97I	Average:73.956; most accessible tissue: Zhenshan97 young leaf, score: 87.004	unknown	unknown	TOLERATED	0.34
vg0103031868	G -> DEL	LOC_Os01g06400.1	N	frameshift_variant	Average:73.956; most accessible tissue: Zhenshan97 young leaf, score: 87.004	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103031868	4.03E-06	NA	mr1064	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
vg0103031868	NA	1.77E-16	mr1118	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
vg0103031868	NA	1.52E-10	mr1128	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
vg0103031868	NA	3.16E-13	mr1239	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
vg0103031868	NA	1.95E-18	mr1242	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
vg0103031868	NA	2.69E-08	mr1442	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
vg0103031868	NA	3.12E-20	mr1580	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
vg0103031868	NA	2.50E-11	mr1751	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
vg0103031868	NA	4.36E-18	mr1767	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
vg0103031868	NA	1.27E-08	mr1779	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
vg0103031868	NA	1.71E-07	mr1810	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
vg0103031868	NA	2.05E-17	mr1825	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
vg0103031868	NA	3.85E-10	mr1904	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