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Detailed information for vg0907035204:

Variant ID: vg0907035204 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7035204
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCGAGAATCCTGTCGTCGTCTCCCGCTGTTGTCTCGGCGCCGGTCTCCATCATCGTCATTGTTATGGTGACGTCCTCGACTAGTATCGTCTGGCACCC[G/A]
CCGTTCGCGATCGTTGTGATCGTGGTGGTTGTGGCAGTTATCACGGTCTCGGTCCTCGTTTGAGCGGTCTCCTCGATCTTTGTTATCATGGCGCCGTGAA

Reverse complement sequence

TTCACGGCGCCATGATAACAAAGATCGAGGAGACCGCTCAAACGAGGACCGAGACCGTGATAACTGCCACAACCACCACGATCACAACGATCGCGAACGG[C/T]
GGGTGCCAGACGATACTAGTCGAGGACGTCACCATAACAATGACGATGATGGAGACCGGCGCCGAGACAACAGCGGGAGACGACGACAGGATTCTCGAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.60%	0.80%	7.30%	5.25%	NA
All Indica	2759	82.10%	0.00%	9.31%	8.55%	NA
All Japonica	1512	94.50%	2.40%	2.91%	0.20%	NA
Aus	269	81.00%	0.00%	15.61%	3.35%	NA
Indica I	595	70.80%	0.00%	18.15%	11.09%	NA
Indica II	465	95.70%	0.00%	1.51%	2.80%	NA
Indica III	913	78.90%	0.00%	8.98%	12.16%	NA
Indica Intermediate	786	86.50%	0.00%	7.63%	5.85%	NA
Temperate Japonica	767	90.50%	4.20%	5.22%	0.13%	NA
Tropical Japonica	504	99.20%	0.00%	0.40%	0.40%	NA
Japonica Intermediate	241	97.50%	1.70%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0907035204	G -> DEL	N	N	silent_mutation	Average:28.953; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0907035204	G -> A	LOC_Os09g12330.1	upstream_gene_variant ; 4103.0bp to feature; MODIFIER	silent_mutation	Average:28.953; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0907035204	G -> A	LOC_Os09g12340.1	intron_variant ; MODIFIER	silent_mutation	Average:28.953; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907035204	5.27E-06	5.27E-06	mr1327	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
vg0907035204	1.06E-06	1.91E-08	mr1549_2	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
vg0907035204	4.77E-06	1.32E-07	mr1757_2	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