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Detailed information for vg0703433029:

Variant ID: vg0703433029 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3433029
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTCACATCACATGCAGCAATTGCTGACATAGGAATCATACCAAAGCGGTCCCCGGTTCTTCTGAATGTCACACACATGTGGCCAATAAGAGGATGAGA[T/C]
GACGAGGGGAAGTTCTGAATAGAAGAGTAGGAAAAAAAAAAGACAGACATGTTAGAAAAGGTCGGTTAGAACAAATTAATTGTTTTTCAGTTACATCTGA

Reverse complement sequence

TCAGATGTAACTGAAAAACAATTAATTTGTTCTAACCGACCTTTTCTAACATGTCTGTCTTTTTTTTTTCCTACTCTTCTATTCAGAACTTCCCCTCGTC[A/G]
TCTCATCCTCTTATTGGCCACATGTGTGTGACATTCAGAAGAACCGGGGACCGCTTTGGTATGATTCCTATGTCAGCAATTGCTGCATGTGATGTGAAGG

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	55.50%	44.20%	0.28%	0.06%	NA
All Indica	2759	35.40%	64.10%	0.43%	0.07%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	84.70%	15.00%	0.34%	0.00%	NA
Indica II	465	15.30%	84.30%	0.22%	0.22%	NA
Indica III	913	15.40%	84.10%	0.44%	0.00%	NA
Indica Intermediate	786	33.10%	66.20%	0.64%	0.13%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	56.70%	41.10%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0703433029	T -> DEL	LOC_Os07g06970.1	N	frameshift_variant	Average:55.153; most accessible tissue: Callus, score: 77.537	N	N	N	N
vg0703433029	T -> C	LOC_Os07g06970.1	synonymous_variant ; p.Ser133Ser; LOW	synonymous_codon	Average:55.153; most accessible tissue: Callus, score: 77.537	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703433029	NA	3.85E-06	mr1130	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
vg0703433029	NA	1.66E-07	mr1291	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
vg0703433029	NA	6.02E-06	mr1531	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
vg0703433029	NA	9.08E-06	mr1679	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
vg0703433029	NA	5.51E-06	mr1904	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
vg0703433029	NA	2.64E-08	mr1170_2	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