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Detailed information for vg0429946042:

Variant ID: vg0429946042 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 29946042
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTGGTCCGAGCTAACTAAAAGAAAGCCAGCTATTAAGACTTCTCGCTCCTGCTAAGGCCCAAGTTTTGGCCTCTTCCTTGATCTTGGCTAAAAGAGAG[A/G]
TAGCTGAAAGCTCCTTCTGTTGGAAGGTTCTGCGATTCCTTTCGCTCCATATCTCCCAGGCGACCAACAACATCAAAGTGCGGAGTGCCTTCTTAGATGT

Reverse complement sequence

ACATCTAAGAAGGCACTCCGCACTTTGATGTTGTTGGTCGCCTGGGAGATATGGAGCGAAAGGAATCGCAGAACCTTCCAACAGAAGGAGCTTTCAGCTA[T/C]
CTCTCTTTTAGCCAAGATCAAGGAAGAGGCCAAAACTTGGGCCTTAGCAGGAGCGAGAAGTCTTAATAGCTGGCTTTCTTTTAGTTAGCTCGGACCAAAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.90%	24.50%	0.32%	0.25%	NA
All Indica	2759	63.60%	35.60%	0.47%	0.33%	NA
All Japonica	1512	99.60%	0.30%	0.07%	0.07%	NA
Aus	269	45.00%	55.00%	0.00%	0.00%	NA
Indica I	595	81.50%	18.30%	0.17%	0.00%	NA
Indica II	465	29.70%	69.00%	0.86%	0.43%	NA
Indica III	913	65.50%	34.00%	0.33%	0.22%	NA
Indica Intermediate	786	68.10%	30.70%	0.64%	0.64%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	72.20%	25.60%	0.00%	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
vg0429946042	A -> DEL	LOC_Os04g50188.1	N	frameshift_variant	Average:51.023; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0429946042	A -> G	LOC_Os04g50188.1	missense_variant ; p.Ile83Thr; MODERATE	nonsynonymous_codon ; I83T	Average:51.023; most accessible tissue: Zhenshan97 panicle, score: 63.607	possibly damaging	-1.622	TOLERATED	0.72

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0429946042	NA	1.37E-11	mr1169	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
vg0429946042	4.07E-07	4.06E-17	mr1174	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
vg0429946042	3.14E-10	3.74E-21	mr1174	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
vg0429946042	7.25E-06	7.74E-09	mr1347	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
vg0429946042	7.75E-08	6.42E-14	mr1347	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
vg0429946042	NA	2.93E-07	mr1354	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
vg0429946042	8.05E-06	5.21E-09	mr1406	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
vg0429946042	1.36E-06	8.92E-15	mr1174_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
vg0429946042	2.79E-11	4.18E-25	mr1174_2	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
vg0429946042	7.54E-08	6.68E-11	mr1347_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
vg0429946042	2.66E-11	1.18E-23	mr1347_2	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
vg0429946042	NA	8.32E-09	mr1354_2	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
vg0429946042	8.12E-06	3.37E-09	mr1406_2	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
vg0429946042	NA	1.58E-06	mr1540_2	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
vg0429946042	NA	2.04E-06	mr1732_2	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