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Detailed information for vg1206162924:

Variant ID: vg1206162924 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6162924
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAGATATTTAACTTATATCGAAGGAGCCTACGCGTCGGGCGCCTGATGGAGGAGTGGAAAAATCGGACGCTGACGTCACGCATGCGCCAGCACGATGT[T/C]
AGCATGATGCATGCGTGCAAAACCACTAAATTTTTTCTCTTAAATTATTTATCCAAATTATGATTCGATTACACCACTAAATTCATTGCAATTAAATCTT

Reverse complement sequence

AAGATTTAATTGCAATGAATTTAGTGGTGTAATCGAATCATAATTTGGATAAATAATTTAAGAGAAAAAATTTAGTGGTTTTGCACGCATGCATCATGCT[A/G]
ACATCGTGCTGGCGCATGCGTGACGTCAGCGTCCGATTTTTCCACTCCTCCATCAGGCGCCCGACGCGTAGGCTCCTTCGATATAAGTTAAATATCTAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.60%	16.70%	0.55%	34.17%	NA
All Indica	2759	68.50%	16.80%	0.18%	14.50%	NA
All Japonica	1512	22.90%	6.10%	1.06%	69.97%	NA
Aus	269	6.30%	48.30%	0.00%	45.35%	NA
Indica I	595	53.30%	19.30%	0.00%	27.39%	NA
Indica II	465	77.80%	7.10%	0.00%	15.05%	NA
Indica III	913	78.10%	17.60%	0.11%	4.16%	NA
Indica Intermediate	786	63.40%	19.70%	0.51%	16.41%	NA
Temperate Japonica	767	27.80%	10.40%	1.17%	60.63%	NA
Tropical Japonica	504	9.50%	0.80%	1.19%	88.49%	NA
Japonica Intermediate	241	35.30%	3.30%	0.41%	61.00%	NA
VI/Aromatic	96	10.40%	87.50%	0.00%	2.08%	NA
Intermediate	90	36.70%	21.10%	5.56%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206162924	T -> C	LOC_Os12g11410.1	upstream_gene_variant ; 2962.0bp to feature; MODIFIER	silent_mutation	Average:7.239; most accessible tissue: Callus, score: 34.959	N	N	N	N
vg1206162924	T -> C	LOC_Os12g11420.1	downstream_gene_variant ; 1511.0bp to feature; MODIFIER	silent_mutation	Average:7.239; most accessible tissue: Callus, score: 34.959	N	N	N	N
vg1206162924	T -> C	LOC_Os12g11410-LOC_Os12g11420	intergenic_region ; MODIFIER	silent_mutation	Average:7.239; most accessible tissue: Callus, score: 34.959	N	N	N	N
vg1206162924	T -> DEL	N	N	silent_mutation	Average:7.239; most accessible tissue: Callus, score: 34.959	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206162924	NA	9.29E-06	mr1336	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
vg1206162924	6.16E-06	4.86E-06	mr1094_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
vg1206162924	8.57E-07	2.32E-06	mr1112_2	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
vg1206162924	NA	1.95E-06	mr1864_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
vg1206162924	6.92E-08	6.92E-08	mr1973_2	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