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Detailed information for vg0434701142:

Variant ID: vg0434701142 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 34701142
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TATCCACTAGTGGCTTTGATCTCATCCACATCAGAGATCCAGTTAGAATCACTATATTCCTCCAGTATCGCAGGATACCCAGTATAGTGAAGCCCCAATT[C/A]
CATAGTACGTTTTAGATAGCGCATTACTCGCTCGAGCGCACGCCAGTGATCATCTCTTGGATTAGAGGTAAACCGGCTCAACTTGCTCACAGCAAAGGAG

Reverse complement sequence

CTCCTTTGCTGTGAGCAAGTTGAGCCGGTTTACCTCTAATCCAAGAGATGATCACTGGCGTGCGCTCGAGCGAGTAATGCGCTATCTAAAACGTACTATG[G/T]
AATTGGGGCTTCACTATACTGGGTATCCTGCGATACTGGAGGAATATAGTGATTCTAACTGGATCTCTGATGTGGATGAGATCAAAGCCACTAGTGGATA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.10%	48.00%	1.69%	0.23%	NA
All Indica	2759	84.00%	12.90%	2.75%	0.36%	NA
All Japonica	1512	1.20%	98.80%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	90.10%	5.70%	3.19%	1.01%	NA
Indica II	465	86.20%	9.70%	4.09%	0.00%	NA
Indica III	913	82.10%	15.10%	2.63%	0.11%	NA
Indica Intermediate	786	80.20%	17.70%	1.78%	0.38%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.40%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	94.80%	1.04%	0.00%	NA
Intermediate	90	31.10%	64.40%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0434701142	C -> DEL	LOC_Os04g58290.1	N	frameshift_variant	Average:27.758; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N
vg0434701142	C -> A	LOC_Os04g58290.1	stop_gained ; p.Glu320*; HIGH	stop_gained	Average:27.758; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0434701142	NA	1.31E-09	mr1011_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
vg0434701142	NA	3.93E-21	mr1164_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
vg0434701142	NA	2.03E-07	mr1321_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
vg0434701142	6.18E-06	NA	mr1322_2	Ind_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
vg0434701142	NA	9.76E-10	mr1349_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
vg0434701142	NA	2.01E-07	mr1376_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
vg0434701142	NA	6.46E-08	mr1431_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
vg0434701142	NA	1.48E-12	mr1521_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
vg0434701142	NA	4.40E-06	mr1655_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
vg0434701142	NA	3.66E-08	mr1885_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
vg0434701142	NA	2.84E-21	mr1924_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
vg0434701142	NA	7.32E-27	mr1943_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