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Detailed information for vg1204260659:

Variant ID: vg1204260659 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4260659
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACTATCCTTGAGCTACACAATATTATTAATCAAGGCCGTGAATCCACATGAACCTGACTTAACCCAAGGCCTACGATGATTCAGACCGAACTGGCAACC[T/C]
GACCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTTGATAAGCAAGTTTTAAGAATTAAACCACTAACTTGGGTACATT

Reverse complement sequence

AATGTACCCAAGTTAGTGGTTTAATTCTTAAAACTTGCTTATCAACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGTC[A/G]
GGTTGCCAGTTCGGTCTGAATCATCGTAGGCCTTGGGTTAAGTCAGGTTCATGTGGATTCACGGCCTTGATTAATAATATTGTGTAGCTCAAGGATAGTG

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	53.50%	23.50%	1.93%	21.10%	NA
All Indica	2759	85.50%	5.10%	1.12%	8.30%	NA
All Japonica	1512	2.70%	55.80%	2.12%	39.35%	NA
Aus	269	29.70%	30.90%	8.18%	31.23%	NA
Indica I	595	91.60%	4.20%	1.01%	3.19%	NA
Indica II	465	81.50%	7.70%	1.94%	8.82%	NA
Indica III	913	86.90%	1.30%	0.66%	11.17%	NA
Indica Intermediate	786	81.60%	8.70%	1.27%	8.52%	NA
Temperate Japonica	767	2.90%	79.90%	3.78%	13.43%	NA
Tropical Japonica	504	2.40%	29.00%	0.40%	68.25%	NA
Japonica Intermediate	241	2.90%	35.30%	0.41%	61.41%	NA
VI/Aromatic	96	10.40%	14.60%	5.21%	69.79%	NA
Intermediate	90	42.20%	32.20%	1.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204260659	T -> C	LOC_Os12g08380.1	upstream_gene_variant ; 1945.0bp to feature; MODIFIER	silent_mutation	Average:56.525; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1204260659	T -> C	LOC_Os12g08390.1	downstream_gene_variant ; 3447.0bp to feature; MODIFIER	silent_mutation	Average:56.525; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1204260659	T -> C	LOC_Os12g08370.1	intron_variant ; MODIFIER	silent_mutation	Average:56.525; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1204260659	T -> DEL	N	N	silent_mutation	Average:56.525; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204260659	6.06E-07	2.47E-08	mr1711_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