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Detailed information for vg0921835488:

Variant ID: vg0921835488 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 21835488
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGGGCGAAGGGAGTACTCCGTTTCCTATGACTATGGATGGGATGTCCAAATTGTTGAAGATGGTGTGTTGGGCGACTTCGGTCATCATCTTCTTTGCGG[G/C]
CATGCTCAGCTGCAAGTGCAACCATGGAAGCTCGGAGAAATCGCTTCTGGCTACCTCCCCAATCGAAACGCCTGATATTGAAAATTCTGCTCCAACTGCT

Reverse complement sequence

AGCAGTTGGAGCAGAATTTTCAATATCAGGCGTTTCGATTGGGGAGGTAGCCAGAAGCGATTTCTCCGAGCTTCCATGGTTGCACTTGCAGCTGAGCATG[C/G]
CCGCAAAGAAGATGATGACCGAAGTCGCCCAACACACCATCTTCAACAATTTGGACATCCCATCCATAGTCATAGGAAACGGAGTACTCCCTTCGCCCCA

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	62.00%	35.10%	0.78%	2.16%	NA
All Indica	2759	96.40%	1.40%	0.54%	1.70%	NA
All Japonica	1512	1.70%	98.30%	0.00%	0.00%	NA
Aus	269	70.30%	1.90%	7.81%	20.07%	NA
Indica I	595	90.80%	1.00%	1.85%	6.39%	NA
Indica II	465	97.00%	2.60%	0.43%	0.00%	NA
Indica III	913	99.50%	0.30%	0.11%	0.11%	NA
Indica Intermediate	786	96.70%	2.20%	0.13%	1.02%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	3.80%	96.20%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	43.30%	54.40%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0921835488	G -> DEL	LOC_Os09g37870.1	N	frameshift_variant	Average:47.384; most accessible tissue: Zhenshan97 flower, score: 78.132	N	N	N	N
vg0921835488	G -> C	LOC_Os09g37870.1	missense_variant ; p.Gly359Ala; MODERATE	nonsynonymous_codon ; G359A	Average:47.384; most accessible tissue: Zhenshan97 flower, score: 78.132	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0921835488	NA	1.09E-26	mr1024	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
vg0921835488	5.04E-06	NA	mr1098	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
vg0921835488	NA	2.84E-28	mr1148	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
vg0921835488	NA	2.21E-15	mr1228	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
vg0921835488	NA	2.11E-15	mr1323	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
vg0921835488	NA	4.94E-11	mr1325	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
vg0921835488	NA	8.88E-13	mr1326	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
vg0921835488	NA	8.51E-16	mr1361	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
vg0921835488	NA	4.47E-14	mr1376	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
vg0921835488	NA	4.47E-14	mr1431	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
vg0921835488	NA	1.51E-40	mr1509	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
vg0921835488	NA	7.16E-09	mr1575	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
vg0921835488	3.90E-06	NA	mr1603	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
vg0921835488	NA	3.08E-07	mr1659	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
vg0921835488	NA	5.50E-06	mr1681	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
vg0921835488	NA	1.80E-08	mr1776	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
vg0921835488	NA	1.94E-06	mr1850	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
vg0921835488	NA	3.74E-12	mr1940	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
vg0921835488	NA	7.78E-23	mr1386_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