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Detailed information for vg1221950143:

Variant ID: vg1221950143 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21950143
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGAAAAGAAATACTTAGATTTAAATTATAGGTGCAAGATGATCAAAGGTGACTTGCCTTGCTCGAGATCTTGAGCTCGATCCTCGAAATCCTCGCACTG[C/T]
GGGTCTGCGGGCTCTGAAACTACACGCGAAACGGGACAACTCAACAAACGGCGAAAACAAAGCCCTATTATTGACCTCTAAGCGTGCCATTAGATCTTGA

Reverse complement sequence

TCAAGATCTAATGGCACGCTTAGAGGTCAATAATAGGGCTTTGTTTTCGCCGTTTGTTGAGTTGTCCCGTTTCGCGTGTAGTTTCAGAGCCCGCAGACCC[G/A]
CAGTGCGAGGATTTCGAGGATCGAGCTCAAGATCTCGAGCAAGGCAAGTCACCTTTGATCATCTTGCACCTATAATTTAAATCTAAGTATTTCTTTTCCA

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	45.30%	3.70%	2.14%	48.88%	NA
All Indica	2759	26.50%	0.40%	2.90%	70.21%	NA
All Japonica	1512	80.80%	10.10%	0.33%	8.73%	NA
Aus	269	20.80%	0.00%	4.46%	74.72%	NA
Indica I	595	15.00%	0.00%	1.18%	83.87%	NA
Indica II	465	55.10%	0.40%	3.01%	41.51%	NA
Indica III	913	17.50%	0.80%	3.61%	78.09%	NA
Indica Intermediate	786	28.60%	0.40%	3.31%	67.68%	NA
Temperate Japonica	767	95.80%	0.40%	0.26%	3.52%	NA
Tropical Japonica	504	53.00%	26.80%	0.60%	19.64%	NA
Japonica Intermediate	241	91.30%	6.20%	0.00%	2.49%	NA
VI/Aromatic	96	76.00%	0.00%	1.04%	22.92%	NA
Intermediate	90	67.80%	8.90%	3.33%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221950143	C -> DEL	N	N	silent_mutation	Average:23.101; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N
vg1221950143	C -> T	LOC_Os12g35930.1	downstream_gene_variant ; 2192.0bp to feature; MODIFIER	silent_mutation	Average:23.101; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N
vg1221950143	C -> T	LOC_Os12g35920-LOC_Os12g35930	intergenic_region ; MODIFIER	silent_mutation	Average:23.101; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221950143	9.14E-07	3.32E-08	mr1557	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
vg1221950143	NA	1.04E-06	mr1583	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