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Detailed information for vg0910616659:

Variant ID: vg0910616659 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10616659
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGCATCACGTGAATGTTTATGGCTTCACAGAATGATTAACCACATATTAACATCTTGTGGTATTGGTTCATTAGAATCACCTACCATTATCTATGAAG[A/G]
TAATGCCGCTTGTGTTGTTTAGATGGAAACTGGTTATATTAAGAGCAACATCACTAAGAATATTGCTCCTAAATTATTTTATCCTCATGAGCTTCAGCAA

Reverse complement sequence

TTGCTGAAGCTCATGAGGATAAAATAATTTAGGAGCAATATTCTTAGTGATGTTGCTCTTAATATAACCAGTTTCCATCTAAACAACACAAGCGGCATTA[T/C]
CTTCATAGATAATGGTAGGTGATTCTAATGAACCAATACCACAAGATGTTAATATGTGGTTAATCATTCTGTGAAGCCATAAACATTCACGTGATGCCTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.60%	4.70%	9.99%	17.67%	NA
All Indica	2759	61.20%	7.40%	14.97%	16.42%	NA
All Japonica	1512	76.50%	0.30%	2.65%	20.57%	NA
Aus	269	84.00%	2.20%	2.97%	10.78%	NA
Indica I	595	66.70%	6.20%	12.10%	14.96%	NA
Indica II	465	49.50%	11.00%	16.99%	22.58%	NA
Indica III	913	64.10%	6.60%	16.65%	12.71%	NA
Indica Intermediate	786	60.60%	7.30%	13.99%	18.19%	NA
Temperate Japonica	767	88.40%	0.40%	2.35%	8.87%	NA
Tropical Japonica	504	61.10%	0.40%	1.79%	36.71%	NA
Japonica Intermediate	241	70.50%	0.00%	5.39%	24.07%	NA
VI/Aromatic	96	67.70%	0.00%	1.04%	31.25%	NA
Intermediate	90	68.90%	6.70%	11.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0910616659	A -> G	LOC_Os09g17329.1	intron_variant ; MODIFIER	silent_mutation	Average:9.075; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0910616659	A -> G	LOC_Os09g17329.2	intron_variant ; MODIFIER	silent_mutation	Average:9.075; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0910616659	A -> DEL	N	N	silent_mutation	Average:9.075; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910616659	2.09E-06	NA	mr1134_2	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
vg0910616659	8.05E-06	5.53E-06	mr1517_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
vg0910616659	NA	4.37E-07	mr1672_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