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Detailed information for vg0334849585:

Variant ID: vg0334849585 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34849585
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTGGAGAACCATGGCGACGGTGACGAGGACCTCGGCTCTCGCCGGAATCCCCACTCCCGGACAGGGTGGGAGTAAATGCCACCGCCTCCTCCTCTACTT[T/C]
CAGGACCTCGACCATGGTCGGCTAAGGCCTGGAGAAAATTGGGACGAAAGAAAGCGACTTCCTCTCGGAATGCGCAACCGCCCCTACTTGGCGCGCCAGC

Reverse complement sequence

GCTGGCGCGCCAAGTAGGGGCGGTTGCGCATTCCGAGAGGAAGTCGCTTTCTTTCGTCCCAATTTTCTCCAGGCCTTAGCCGACCATGGTCGAGGTCCTG[A/G]
AAGTAGAGGAGGAGGCGGTGGCATTTACTCCCACCCTGTCCGGGAGTGGGGATTCCGGCGAGAGCCGAGGTCCTCGTCACCGTCGCCATGGTTCTCCAAC

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	55.40%	42.60%	2.03%	0.00%	NA
All Indica	2759	83.90%	13.00%	3.04%	0.00%	NA
All Japonica	1512	2.10%	97.70%	0.26%	0.00%	NA
Aus	269	82.20%	17.10%	0.74%	0.00%	NA
Indica I	595	91.90%	6.60%	1.51%	0.00%	NA
Indica II	465	86.90%	12.70%	0.43%	0.00%	NA
Indica III	913	81.10%	14.70%	4.27%	0.00%	NA
Indica Intermediate	786	79.50%	16.20%	4.33%	0.00%	NA
Temperate Japonica	767	0.50%	99.30%	0.13%	0.00%	NA
Tropical Japonica	504	4.60%	94.80%	0.60%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	15.60%	84.40%	0.00%	0.00%	NA
Intermediate	90	40.00%	53.30%	6.67%	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
vg0334849585	T -> C	LOC_Os03g61400.1	missense_variant ; p.Lys6Glu; MODERATE	nonsynonymous_codon ; K6E	Average:46.743; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334849585	NA	1.88E-06	mr1278	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
vg0334849585	NA	2.58E-06	mr1508	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
vg0334849585	NA	5.14E-09	mr1575	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
vg0334849585	NA	3.16E-07	mr1646	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
vg0334849585	NA	3.71E-07	mr1739	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
vg0334849585	NA	2.01E-07	mr1781	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
vg0334849585	NA	4.00E-07	mr1748_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
vg0334849585	1.43E-07	3.88E-06	mr1748_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