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Detailed information for vg1125875287:

Variant ID: vg1125875287 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25875287
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGATAAAACAAAGTCACAAGAAAAAATGGCCAAAATAGTACTAGTAAGAACACAATAACATGATAGAGCATGATTTTAGAAACATTTAGGAAAAAGAAT[A/C]
ATCCAATTTAAAGTTCATATGAGTGAGATACACTAGTTTTAATTTTTTTAAATTTTTCAAATTTTATTTTCGCATATGGCTCCTTAAGACACCTGTATGG

Reverse complement sequence

CCATACAGGTGTCTTAAGGAGCCATATGCGAAAATAAAATTTGAAAAATTTAAAAAAATTAAAACTAGTGTATCTCACTCATATGAACTTTAAATTGGAT[T/G]
ATTCTTTTTCCTAAATGTTTCTAAAATCATGCTCTATCATGTTATTGTGTTCTTACTAGTACTATTTTGGCCATTTTTTCTTGTGACTTTGTTTTATCAA

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	38.30%	24.30%	0.25%	37.11%	NA
All Indica	2759	55.10%	15.00%	0.22%	29.72%	NA
All Japonica	1512	11.40%	39.70%	0.20%	48.61%	NA
Aus	269	27.50%	23.00%	0.37%	49.07%	NA
Indica I	595	53.40%	42.70%	0.50%	3.36%	NA
Indica II	465	36.60%	5.40%	0.43%	57.63%	NA
Indica III	913	61.90%	5.10%	0.00%	32.97%	NA
Indica Intermediate	786	59.40%	11.10%	0.13%	29.39%	NA
Temperate Japonica	767	7.60%	61.40%	0.13%	30.90%	NA
Tropical Japonica	504	18.30%	6.20%	0.20%	75.40%	NA
Japonica Intermediate	241	9.50%	41.10%	0.41%	48.96%	NA
VI/Aromatic	96	3.10%	52.10%	0.00%	44.79%	NA
Intermediate	90	46.70%	24.40%	2.22%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125875287	A -> DEL	N	N	silent_mutation	Average:26.536; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg1125875287	A -> C	LOC_Os11g42930.1	downstream_gene_variant ; 2480.0bp to feature; MODIFIER	silent_mutation	Average:26.536; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg1125875287	A -> C	LOC_Os11g42920.1	intron_variant ; MODIFIER	silent_mutation	Average:26.536; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125875287	NA	8.08E-06	mr1060	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
vg1125875287	4.40E-07	3.82E-11	mr1191	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
vg1125875287	5.75E-08	1.92E-08	mr1191	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
vg1125875287	NA	9.58E-08	mr1332	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
vg1125875287	NA	3.59E-06	mr1380	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
vg1125875287	NA	5.04E-06	mr1561	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
vg1125875287	NA	1.47E-06	mr1570	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
vg1125875287	NA	2.44E-06	mr1614	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
vg1125875287	1.58E-07	1.54E-13	mr1644	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
vg1125875287	5.05E-08	4.79E-09	mr1644	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
vg1125875287	NA	5.93E-09	mr1937	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
vg1125875287	NA	2.82E-06	mr1057_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
vg1125875287	1.85E-06	1.39E-14	mr1191_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
vg1125875287	8.02E-08	6.91E-09	mr1191_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
vg1125875287	NA	5.14E-06	mr1332_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