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Detailed information for vg0431889500:

Variant ID: vg0431889500 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31889500
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGAGACCTCCAAGCTTTCATGACAAGGCATTTCCAAAGCCGACACAGGTTTACCATATGCCGACGAGAGGGGTCCCAGACCAACAACAGGTTAGGTCC[T/C]
AGACCATACTGTGCCAGGAAGCCTAGGGGTCCTCCCTGACACCACCCCGGCAAATCCACAAGTCTCTCGGCATCAAGGCTCCCCTGATAAGCTAGTTACT

Reverse complement sequence

AGTAACTAGCTTATCAGGGGAGCCTTGATGCCGAGAGACTTGTGGATTTGCCGGGGTGGTGTCAGGGAGGACCCCTAGGCTTCCTGGCACAGTATGGTCT[A/G]
GGACCTAACCTGTTGTTGGTCTGGGACCCCTCTCGTCGGCATATGGTAAACCTGTGTCGGCTTTGGAAATGCCTTGTCATGAAAGCTTGGAGGTCTCCCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	15.70%	11.40%	20.36%	52.62%	NA
All Indica	2759	7.40%	11.40%	28.05%	53.17%	NA
All Japonica	1512	33.70%	13.30%	6.35%	46.63%	NA
Aus	269	4.10%	4.50%	17.47%	73.98%	NA
Indica I	595	9.70%	5.50%	16.97%	67.73%	NA
Indica II	465	9.50%	3.40%	16.56%	70.54%	NA
Indica III	913	6.80%	19.70%	42.39%	31.11%	NA
Indica Intermediate	786	5.10%	10.80%	26.59%	57.51%	NA
Temperate Japonica	767	52.00%	25.30%	10.82%	11.86%	NA
Tropical Japonica	504	7.70%	0.80%	0.60%	90.87%	NA
Japonica Intermediate	241	29.90%	1.20%	4.15%	64.73%	NA
VI/Aromatic	96	0.00%	1.00%	27.08%	71.88%	NA
Intermediate	90	16.70%	10.00%	21.11%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0431889500	T -> C	LOC_Os04g53520.1	intron_variant ; MODIFIER	silent_mutation	Average:9.031; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0431889500	T -> DEL	N	N	silent_mutation	Average:9.031; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431889500	NA	8.81E-07	mr1063	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
vg0431889500	9.10E-06	9.09E-06	mr1122	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
vg0431889500	NA	8.14E-07	mr1280	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
vg0431889500	8.11E-08	2.58E-07	mr1318	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
vg0431889500	3.00E-06	1.02E-08	mr1318	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
vg0431889500	NA	5.23E-06	mr1482	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
vg0431889500	NA	5.96E-06	mr1503	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
vg0431889500	NA	1.17E-07	mr1531	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
vg0431889500	NA	1.53E-06	mr1788	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