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Detailed information for vg0305008708:

Variant ID: vg0305008708 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 5008708
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTCCTGTACCGCTGCTTCCACTTGAGGCCTCCAGCTATTCACCCCTTGTTCCATCTTGACGACGGCTGCTTGAGTCTCACCTTGAGCTTGATTCAACG[T/C]
CACCAGGGACTCCTGAATCTCCAGCAACACCTTGCCGAATCGATGTTCTGCTTCTCCATCGCCTCTACTTGAAGCTGCAATCGGGAGGTATAGCATGGCT

Reverse complement sequence

AGCCATGCTATACCTCCCGATTGCAGCTTCAAGTAGAGGCGATGGAGAAGCAGAACATCGATTCGGCAAGGTGTTGCTGGAGATTCAGGAGTCCCTGGTG[A/G]
CGTTGAATCAAGCTCAAGGTGAGACTCAAGCAGCCGTCGTCAAGATGGAACAAGGGGTGAATAGCTGGAGGCCTCAAGTGGAAGCAGCGGTACAGGAACT

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	90.20%	5.70%	3.49%	0.57%	NA
All Indica	2759	99.30%	0.00%	0.07%	0.54%	NA
All Japonica	1512	71.80%	17.50%	10.65%	0.07%	NA
Aus	269	97.80%	0.00%	0.00%	2.23%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	98.40%	0.00%	0.00%	1.64%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	49.40%	31.00%	19.56%	0.00%	NA
Tropical Japonica	504	97.40%	1.40%	1.19%	0.00%	NA
Japonica Intermediate	241	89.60%	7.90%	2.07%	0.41%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	92.20%	4.40%	2.22%	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
vg0305008708	T -> C	LOC_Os03g10000.1	missense_variant ; p.Thr33Ala; MODERATE	nonsynonymous_codon ; T33A	Average:46.96; most accessible tissue: Zhenshan97 young leaf, score: 74.302	unknown	unknown	TOLERATED	1.00
vg0305008708	T -> DEL	LOC_Os03g10000.1	N	frameshift_variant	Average:46.96; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0305008708	NA	6.38E-07	mr1401	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
vg0305008708	5.37E-07	NA	mr1765	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