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Detailed information for vg0619176470:

Variant ID: vg0619176470 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19176470
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTTCTATCTGTGACGGCCTCTAACATGCCTAGAAATAGCGGGCCGTCACAAGGAAGTTATCGCAATCAGGCCGAAAAAGTGCCCGATTGAGATATGGTC[A/G]
CACCCATATGTTAGATGGGCATAAAACTTAAGCCCGTCACGGATGACATCTATCAGTGACGGGCCGTAGTTTAGACTCGATTGAGATAACATTCCATATC

Reverse complement sequence

GATATGGAATGTTATCTCAATCGAGTCTAAACTACGGCCCGTCACTGATAGATGTCATCCGTGACGGGCTTAAGTTTTATGCCCATCTAACATATGGGTG[T/C]
GACCATATCTCAATCGGGCACTTTTTCGGCCTGATTGCGATAACTTCCTTGTGACGGCCCGCTATTTCTAGGCATGTTAGAGGCCGTCACAGATAGAAGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.60%	30.50%	0.11%	5.80%	NA
All Indica	2759	90.40%	9.20%	0.04%	0.40%	NA
All Japonica	1512	6.60%	76.10%	0.20%	17.13%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	97.50%	1.00%	0.00%	1.51%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	85.90%	14.00%	0.11%	0.00%	NA
Indica Intermediate	786	86.90%	12.80%	0.00%	0.25%	NA
Temperate Japonica	767	3.90%	70.70%	0.39%	25.03%	NA
Tropical Japonica	504	11.30%	85.30%	0.00%	3.37%	NA
Japonica Intermediate	241	5.40%	73.90%	0.00%	20.75%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	65.60%	31.10%	0.00%	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
vg0619176470	A -> G	LOC_Os06g32920-LOC_Os06g32944	intergenic_region ; MODIFIER	silent_mutation	Average:58.235; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0619176470	A -> DEL	N	N	silent_mutation	Average:58.235; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619176470	7.36E-07	NA	mr1033	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
vg0619176470	NA	7.50E-06	mr1104	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
vg0619176470	NA	4.30E-11	mr1138	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
vg0619176470	NA	9.26E-09	mr1301	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
vg0619176470	NA	1.87E-10	mr1354	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
vg0619176470	NA	2.66E-13	mr1900	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
vg0619176470	NA	6.19E-06	mr1900	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
vg0619176470	NA	2.97E-08	mr1155_2	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
vg0619176470	NA	2.13E-06	mr1269_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
vg0619176470	NA	9.28E-12	mr1354_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
vg0619176470	NA	5.75E-06	mr1354_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
vg0619176470	NA	1.09E-06	mr1456_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
vg0619176470	NA	5.27E-08	mr1624_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
vg0619176470	NA	8.04E-15	mr1686_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