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Detailed information for vg1209004409:

Variant ID: vg1209004409 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9004409
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.36, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

GCGATGGCAGCCGCCGGAAGTGAAGACATGGTCGCCATCAACAACGGCAGCGGATTACACCAACCGTGGAGGCGAAGAAACCGGTCGGCAGTGATGACGG[C/T]
GGCCAGCGATGAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAGTGGACGAGGCGGCCGGTCAGTG

Reverse complement sequence

CACTGACCGGCCGCCTCGTCCACTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTCATCGCTGGCC[G/A]
CCGTCATCACTGCCGACCGGTTTCTTCGCCTCCACGGTTGGTGTAATCCGCTGCCGTTGTTGATGGCGACCATGTCTTCACTTCCGGCGGCTGCCATCGC

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	39.80%	38.10%	0.47%	21.67%	NA
All Indica	2759	54.00%	10.30%	0.76%	34.87%	NA
All Japonica	1512	4.40%	94.50%	0.00%	1.06%	NA
Aus	269	81.40%	5.60%	0.37%	12.64%	NA
Indica I	595	36.30%	21.30%	0.34%	42.02%	NA
Indica II	465	51.60%	12.30%	1.29%	34.84%	NA
Indica III	913	65.30%	2.70%	0.22%	31.76%	NA
Indica Intermediate	786	55.90%	9.70%	1.40%	33.08%	NA
Temperate Japonica	767	6.00%	93.00%	0.00%	1.04%	NA
Tropical Japonica	504	3.60%	95.60%	0.00%	0.79%	NA
Japonica Intermediate	241	1.20%	97.10%	0.00%	1.66%	NA
VI/Aromatic	96	72.90%	22.90%	0.00%	4.17%	NA
Intermediate	90	36.70%	54.40%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209004409	C -> DEL	LOC_Os12g15770.1	N	frameshift_variant	Average:40.633; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N
vg1209004409	C -> T	LOC_Os12g15770.1	missense_variant ; p.Ala77Thr; MODERATE	nonsynonymous_codon ; A77T	Average:40.633; most accessible tissue: Zhenshan97 young leaf, score: 69.263	unknown	unknown	TOLERATED	0.25

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209004409	NA	7.08E-08	mr1425	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
vg1209004409	NA	1.54E-07	mr1659	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