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Detailed information for vg0417381371:

Variant ID: vg0417381371 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17381371
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCAAGGCACCAAGGAAGAGGTTAGATTTAGATATCACCTTTCATTTATATGCCACATACTTTTGTTTTGTCAGTGGTATGCCAACAGATAGATTGCAA[C/T]
AGGACACGGTCTTCTCCAGGAAGTGCTACGGTCAAAAAACTTTTCAAGGAAGATGATGAGCAAAAGGGTGAAAAGTGGTATTCCTCTTCCCCTTCACACG

Reverse complement sequence

CGTGTGAAGGGGAAGAGGAATACCACTTTTCACCCTTTTGCTCATCATCTTCCTTGAAAAGTTTTTTGACCGTAGCACTTCCTGGAGAAGACCGTGTCCT[G/A]
TTGCAATCTATCTGTTGGCATACCACTGACAAAACAAAAGTATGTGGCATATAAATGAAAGGTGATATCTAAATCTAACCTCTTCCTTGGTGCCTTGGAA

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	46.00%	43.30%	4.02%	6.71%	NA
All Indica	2759	20.70%	71.80%	4.57%	2.94%	NA
All Japonica	1512	81.50%	0.70%	3.17%	14.62%	NA
Aus	269	91.10%	5.60%	1.49%	1.86%	NA
Indica I	595	23.50%	54.50%	10.76%	11.26%	NA
Indica II	465	42.80%	53.50%	3.44%	0.22%	NA
Indica III	913	4.70%	94.40%	0.44%	0.44%	NA
Indica Intermediate	786	24.00%	69.50%	5.34%	1.15%	NA
Temperate Japonica	767	70.10%	0.30%	4.56%	25.03%	NA
Tropical Japonica	504	97.60%	1.20%	0.99%	0.20%	NA
Japonica Intermediate	241	83.80%	1.20%	3.32%	11.62%	NA
VI/Aromatic	96	64.60%	22.90%	5.21%	7.29%	NA
Intermediate	90	68.90%	20.00%	7.78%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417381371	C -> DEL	N	N	silent_mutation	Average:28.661; most accessible tissue: Minghui63 flag leaf, score: 41.254	N	N	N	N
vg0417381371	C -> T	LOC_Os04g29310.1	intron_variant ; MODIFIER	silent_mutation	Average:28.661; most accessible tissue: Minghui63 flag leaf, score: 41.254	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417381371	NA	1.04E-08	mr1047	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
vg0417381371	NA	7.49E-06	mr1189	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
vg0417381371	NA	3.39E-06	mr1625	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
vg0417381371	1.72E-06	7.71E-08	mr1864	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
vg0417381371	NA	5.25E-06	mr1677_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