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Detailed information for vg0403055835:

Variant ID: vg0403055835 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3055835
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

TCACCCAATGAGGCATTGTTTGGTCGACGATATCGAACTCCACTAATGTGGTCCGAGACTGGAGAACGGGCAGTATTTGGACCTGACATTATCCAAGAAG[C/A]
CGAGGAAAAGGTTCGCCTGATTCGTGACCGTCTAAAAGTAGCGCAATCACGACAAAAGAGTTACGCCGACACCCGAAGAAGAAACCTGGAATTTAAGGAG

Reverse complement sequence

CTCCTTAAATTCCAGGTTTCTTCTTCGGGTGTCGGCGTAACTCTTTTGTCGTGATTGCGCTACTTTTAGACGGTCACGAATCAGGCGAACCTTTTCCTCG[G/T]
CTTCTTGGATAATGTCAGGTCCAAATACTGCCCGTTCTCCAGTCTCGGACCACATTAGTGGAGTTCGATATCGTCGACCAAACAATGCCTCATTGGGTGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.20%	0.20%	2.73%	9.86%	NA
All Indica	2759	82.30%	0.40%	3.99%	13.27%	NA
All Japonica	1512	93.80%	0.00%	0.33%	5.82%	NA
Aus	269	95.50%	0.00%	4.09%	0.37%	NA
Indica I	595	50.10%	0.80%	8.40%	40.67%	NA
Indica II	465	86.90%	0.20%	3.23%	9.68%	NA
Indica III	913	95.90%	0.00%	2.19%	1.86%	NA
Indica Intermediate	786	88.30%	0.60%	3.18%	7.89%	NA
Temperate Japonica	767	89.00%	0.00%	0.26%	10.69%	NA
Tropical Japonica	504	99.40%	0.00%	0.40%	0.20%	NA
Japonica Intermediate	241	97.50%	0.00%	0.41%	2.07%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	0.00%	3.33%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403055835	C -> DEL	LOC_Os04g05900.1	N	frameshift_variant	Average:20.151; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg0403055835	C -> A	LOC_Os04g05900.1	missense_variant ; p.Ala1078Asp; MODERATE	nonsynonymous_codon ; A1078D	Average:20.151; most accessible tissue: Minghui63 young leaf, score: 36.684	probably damaging	2.254	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403055835	3.32E-06	6.88E-06	mr1851_2	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