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Detailed information for vg1215306171:

Variant ID: vg1215306171 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15306171
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTGGGCACCTCAAATCCTTGCGGGTATGGGACTGAATCTACATATTCAGGATACGGCCTTTGATATGTATGCATAACTACTTTGGATTCTATTGCACCA[C/A]
TATCCCGCAAGACATTGTCATCATCTTTTCTAACATCCACATGACCGATTTGTGATTCGATCTTAGGTGACAATGCTATTTCACTTTCGCTTGTGGTACA

Reverse complement sequence

TGTACCACAAGCGAAAGTGAAATAGCATTGTCACCTAAGATCGAATCACAAATCGGTCATGTGGATGTTAGAAAAGATGATGACAATGTCTTGCGGGATA[G/T]
TGGTGCAATAGAATCCAAAGTAGTTATGCATACATATCAAAGGCCGTATCCTGAATATGTAGATTCAGTCCCATACCCGCAAGGATTTGAGGTGCCCAAC

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	68.80%	0.00%	2.69%	28.52%	NA
All Indica	2759	57.40%	0.00%	4.31%	38.27%	NA
All Japonica	1512	91.90%	0.10%	0.53%	7.54%	NA
Aus	269	48.00%	0.00%	0.00%	52.04%	NA
Indica I	595	42.50%	0.00%	9.24%	48.24%	NA
Indica II	465	85.20%	0.00%	1.29%	13.55%	NA
Indica III	913	49.70%	0.00%	4.38%	45.89%	NA
Indica Intermediate	786	61.20%	0.00%	2.29%	36.51%	NA
Temperate Japonica	767	97.40%	0.00%	0.26%	2.35%	NA
Tropical Japonica	504	83.30%	0.00%	0.60%	16.07%	NA
Japonica Intermediate	241	92.10%	0.40%	1.24%	6.22%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	73.30%	0.00%	0.00%	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
vg1215306171	C -> DEL	LOC_Os12g26260.1	N	frameshift_variant	Average:21.107; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg1215306171	C -> A	LOC_Os12g26260.1	missense_variant ; p.Ser392Ile; MODERATE	nonsynonymous_codon ; S392I	Average:21.107; most accessible tissue: Minghui63 panicle, score: 46.754	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215306171	NA	1.42E-06	mr1538	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
vg1215306171	1.29E-10	2.82E-15	mr1547	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
vg1215306171	7.99E-09	1.33E-12	mr1547	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
vg1215306171	2.40E-10	4.25E-21	mr1709	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
vg1215306171	1.73E-08	7.89E-19	mr1709	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
vg1215306171	7.48E-07	NA	mr1004_2	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
vg1215306171	2.06E-06	NA	mr1004_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
vg1215306171	NA	6.01E-07	mr1538_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
vg1215306171	4.52E-07	1.85E-11	mr1547_2	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
vg1215306171	8.20E-07	7.86E-11	mr1547_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
vg1215306171	3.66E-08	1.35E-30	mr1709_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
vg1215306171	2.71E-06	5.80E-23	mr1709_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