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Detailed information for vg0429950476:

Variant ID: vg0429950476 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 29950476
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, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGGCGATGACCCACCGGTTGCTTGCGTCAGTGCTGGTGGTGTTCGGTTGTGCGTTCCTGGCGAGGGAGCAGCAGCGACCTTCTCCGTTGCTTCGTGGG[C/A]
CGGCGTCTTGAAGATGGGCTGACGTGGTGAGACCGAACTATAACGCGTGTAGGGGTCATGAAGACAAAAACAAATAGTATGAGTGGAGGAAAGAGGAACA

Reverse complement sequence

TGTTCCTCTTTCCTCCACTCATACTATTTGTTTTTGTCTTCATGACCCCTACACGCGTTATAGTTCGGTCTCACCACGTCAGCCCATCTTCAAGACGCCG[G/T]
CCCACGAAGCAACGGAGAAGGTCGCTGCTGCTCCCTCGCCAGGAACGCACAACCGAACACCACCAGCACTGACGCAAGCAACCGGTGGGTCATCGCCAAC

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	90.70%	6.00%	3.32%	0.00%	NA
All Indica	2759	94.50%	2.10%	3.48%	0.00%	NA
All Japonica	1512	82.10%	14.20%	3.77%	0.00%	NA
Aus	269	98.10%	0.40%	1.49%	0.00%	NA
Indica I	595	86.70%	3.90%	9.41%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.60%	0.10%	0.33%	0.00%	NA
Indica Intermediate	786	91.30%	4.20%	4.45%	0.00%	NA
Temperate Japonica	767	66.50%	26.50%	7.04%	0.00%	NA
Tropical Japonica	504	99.00%	0.60%	0.40%	0.00%	NA
Japonica Intermediate	241	96.30%	3.30%	0.41%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0429950476	C -> A	LOC_Os04g50192.1	missense_variant ; p.Ala60Ser; MODERATE	nonsynonymous_codon ; A60S	Average:66.374; most accessible tissue: Zhenshan97 young leaf, score: 78.044	unknown	unknown	TOLERATED	0.36

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0429950476	8.64E-06	1.37E-20	Awn_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0429950476	1.07E-06	NA	mr1926	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
vg0429950476	4.67E-06	4.67E-06	mr1166_2	Jap_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
vg0429950476	NA	9.34E-06	mr1167_2	Jap_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
vg0429950476	NA	1.26E-06	mr1305_2	Jap_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
vg0429950476	NA	6.86E-07	mr1585_2	Jap_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
vg0429950476	NA	6.35E-06	mr1765_2	Jap_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
vg0429950476	NA	3.11E-06	mr1780_2	Jap_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