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Detailed information for vg1221741274:

Variant ID: vg1221741274 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21741274
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.33, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

CACAGCATCTCTTTCTCCAAATCTGGGACAAAGCTCTCATGATCTCCGCGTGCCCTTGTTCTTCGCCAGTACACCGTACTGATAGGCACGTTATCCCGCA[C/T]
AACCCAACCGCTATGACGTACATAGTTCTTGGCAGCTTCGGCCGGGGCACTAGGACGTCCATCTTCTTCCACTTCCATTATGATGTGCCGACCCTCAAGC

Reverse complement sequence

GCTTGAGGGTCGGCACATCATAATGGAAGTGGAAGAAGATGGACGTCCTAGTGCCCCGGCCGAAGCTGCCAAGAACTATGTACGTCATAGCGGTTGGGTT[G/A]
TGCGGGATAACGTGCCTATCAGTACGGTGTACTGGCGAAGAACAAGGGCACGCGGAGATCATGAGAGCTTTGTCCCAGATTTGGAGAAAGAGATGCTGTG

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	45.90%	26.20%	17.56%	10.37%	NA
All Indica	2759	39.40%	25.60%	23.63%	11.34%	NA
All Japonica	1512	61.20%	33.70%	1.52%	3.57%	NA
Aus	269	14.50%	1.50%	44.24%	39.78%	NA
Indica I	595	32.60%	49.10%	2.69%	15.63%	NA
Indica II	465	24.30%	12.90%	45.59%	17.20%	NA
Indica III	913	51.30%	18.10%	24.21%	6.46%	NA
Indica Intermediate	786	39.80%	24.00%	25.83%	10.31%	NA
Temperate Japonica	767	71.60%	25.00%	1.30%	2.09%	NA
Tropical Japonica	504	59.90%	31.70%	1.79%	6.55%	NA
Japonica Intermediate	241	31.10%	65.10%	1.66%	2.07%	NA
VI/Aromatic	96	62.50%	4.20%	19.79%	13.54%	NA
Intermediate	90	61.10%	16.70%	18.89%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221741274	C -> DEL	LOC_Os12g35720.1	N	frameshift_variant	Average:27.992; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg1221741274	C -> T	LOC_Os12g35720.1	missense_variant ; p.Val27Met; MODERATE	nonsynonymous_codon ; V27M	Average:27.992; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221741274	2.41E-06	2.11E-07	mr1500	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
vg1221741274	NA	7.01E-06	mr1514	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