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Detailed information for vg0901346489:

Variant ID: vg0901346489 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1346489
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCTTGAGTTCAGGGTATCGAGCTACGAGCTCAGCATGCAAGAGGAGGTGGCAAGGAAGGTTGATGAACGCATGGCCGCACATCGGTCCCATGATCCCCA[G/A]
CCGACCATTCCTCCTGCAATGCTGAGCCCATCAGGAAATCGTAGGAGCTGCGCCTCAACGGGGCAGGTAGGATCACAGAGCATGGACACCATGCAAACCC

Reverse complement sequence

GGGTTTGCATGGTGTCCATGCTCTGTGATCCTACCTGCCCCGTTGAGGCGCAGCTCCTACGATTTCCTGATGGGCTCAGCATTGCAGGAGGAATGGTCGG[C/T]
TGGGGATCATGGGACCGATGTGCGGCCATGCGTTCATCAACCTTCCTTGCCACCTCCTCTTGCATGCTGAGCTCGTAGCTCGATACCCTGAACTCAAGAT

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	82.80%	0.50%	12.78%	3.94%	NA
All Indica	2759	95.30%	0.00%	2.25%	2.39%	NA
All Japonica	1512	67.50%	1.40%	24.21%	6.94%	NA
Aus	269	59.50%	0.00%	40.52%	0.00%	NA
Indica I	595	91.40%	0.00%	1.51%	7.06%	NA
Indica II	465	97.20%	0.00%	2.15%	0.65%	NA
Indica III	913	98.10%	0.00%	1.75%	0.11%	NA
Indica Intermediate	786	93.90%	0.10%	3.44%	2.54%	NA
Temperate Japonica	767	97.80%	0.00%	1.69%	0.52%	NA
Tropical Japonica	504	28.40%	3.20%	55.75%	12.70%	NA
Japonica Intermediate	241	52.70%	2.10%	29.88%	15.35%	NA
VI/Aromatic	96	36.50%	0.00%	50.00%	13.54%	NA
Intermediate	90	76.70%	0.00%	21.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901346489	G -> DEL	LOC_Os09g02870.1	N	frameshift_variant	Average:37.717; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N
vg0901346489	G -> A	LOC_Os09g02870.1	synonymous_variant ; p.Gln379Gln; LOW	synonymous_codon	Average:37.717; most accessible tissue: Zhenshan97 flag leaf, score: 81.985	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901346489	NA	8.18E-07	mr1206	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
vg0901346489	NA	3.06E-07	mr1229	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
vg0901346489	NA	2.28E-07	mr1229	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
vg0901346489	9.09E-08	NA	mr1238	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
vg0901346489	NA	2.64E-06	mr1248	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
vg0901346489	NA	4.97E-06	mr1425	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
vg0901346489	NA	2.45E-08	mr1596	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
vg0901346489	NA	1.17E-06	mr1596	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
vg0901346489	NA	1.48E-06	mr1880	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
vg0901346489	2.05E-10	NA	mr1238_2	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
vg0901346489	1.04E-11	NA	mr1484_2	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
vg0901346489	8.46E-06	NA	mr1609_2	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
vg0901346489	3.28E-08	NA	mr1841_2	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
vg0901346489	2.19E-06	NA	mr1900_2	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
vg0901346489	3.91E-09	NA	mr1945_2	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