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Detailed information for vg0710366378:

Variant ID: vg0710366378 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10366378
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, C: 0.07, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGAACAGATATTGTACGATACAATCGCGGAGGGAAGCAGCCAGTACTGGAACGAAGAAGAGGGGAATGAGGATCCAAACCAGTACTTGAACGAGGAAG[G/C]
GAACGTGAAGAAGGATGCGGAGGGGAACCAGGAGGGGAACGTGGAGAGGGATGTGGAGGGGAACCAGGAGGAGGAGGCTAGTGGAAGTCAACCCTCCGCT

Reverse complement sequence

AGCGGAGGGTTGACTTCCACTAGCCTCCTCCTCCTGGTTCCCCTCCACATCCCTCTCCACGTTCCCCTCCTGGTTCCCCTCCGCATCCTTCTTCACGTTC[C/G]
CTTCCTCGTTCAAGTACTGGTTTGGATCCTCATTCCCCTCTTCTTCGTTCCAGTACTGGCTGCTTCCCTCCGCGATTGTATCGTACAATATCTGTTCCTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.30%	40.60%	10.66%	7.51%	NA
All Indica	2759	67.50%	8.20%	13.19%	11.13%	NA
All Japonica	1512	0.90%	95.60%	0.93%	2.65%	NA
Aus	269	13.80%	62.80%	22.30%	1.12%	NA
Indica I	595	68.10%	6.90%	16.13%	8.91%	NA
Indica II	465	61.50%	5.20%	16.13%	17.20%	NA
Indica III	913	75.00%	4.70%	9.53%	10.73%	NA
Indica Intermediate	786	62.00%	14.90%	13.49%	9.67%	NA
Temperate Japonica	767	1.00%	98.00%	0.65%	0.26%	NA
Tropical Japonica	504	0.40%	91.10%	1.19%	7.34%	NA
Japonica Intermediate	241	1.20%	97.10%	1.24%	0.41%	NA
VI/Aromatic	96	9.40%	34.40%	56.25%	0.00%	NA
Intermediate	90	31.10%	50.00%	13.33%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710366378	G -> DEL	LOC_Os07g17530.1	N	frameshift_variant	Average:23.806; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0710366378	G -> C	LOC_Os07g17530.1	missense_variant ; p.Gly914Ala; MODERATE	nonsynonymous_codon ; G914A	Average:23.806; most accessible tissue: Minghui63 young leaf, score: 32.638	benign	1.408	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710366378	NA	2.87E-21	mr1051	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
vg0710366378	2.72E-06	4.99E-37	mr1828	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