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Detailed information for vg0103433293:

Variant ID: vg0103433293 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3433293
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGTGTCTATATGTAGCATCGACTCCAACTTCTTAAACCACTTGTCTTTGGGCAACGGACCAGAGAAGTTATTTGAGGATATGTCAATAATTATTGCAT[T/C]
TGGAAATGCACATGTGCTTTCTTCATCGGTGAGAGATTGAACGACATGTCCAAATAGCTTATTGGATTTCAGTACAAGCACTTGGAGTCTACGAAGTTTA

Reverse complement sequence

TAAACTTCGTAGACTCCAAGTGCTTGTACTGAAATCCAATAAGCTATTTGGACATGTCGTTCAATCTCTCACCGATGAAGAAAGCACATGTGCATTTCCA[A/G]
ATGCAATAATTATTGACATATCCTCAAATAACTTCTCTGGTCCGTTGCCCAAAGACAAGTGGTTTAAGAAGTTGGAGTCGATGCTACATATAGACACAAA

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	98.80%	0.00%	0.83%	0.34%	NA
All Indica	2759	99.80%	0.00%	0.18%	0.00%	NA
All Japonica	1512	97.40%	0.10%	1.52%	1.06%	NA
Aus	269	95.90%	0.40%	3.72%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.00%	0.64%	0.00%	NA
Temperate Japonica	767	95.80%	0.10%	2.09%	1.96%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	97.10%	0.00%	2.49%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103433293	T -> DEL	LOC_Os01g07280.1	N	frameshift_variant	Average:60.103; most accessible tissue: Callus, score: 91.252	N	N	N	N
vg0103433293	T -> C	LOC_Os01g07280.1	missense_variant ; p.Asn632Asp; MODERATE	nonsynonymous_codon	Average:60.103; most accessible tissue: Callus, score: 91.252	unknown	unknown	TOLERATED	0.22

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103433293	NA	7.07E-06	mr1245	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
vg0103433293	1.43E-06	1.43E-06	mr1373	Jap_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
vg0103433293	NA	2.78E-06	mr1648	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