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Detailed information for vg0801870143:

Variant ID: vg0801870143 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1870143
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGAATACAAGAAAGTGGAACGTGAAGTCTGTTCGACATGGCAGGGGGCTGCACCTAATATGAAGTGGTCTGAACAGAAGATAGAATTTTCGGAAGAAGA[G/C]
CATCCCAAGACTGCCGTTATCCCAGGACGCTATCCGATCGTGGTCGAGCCCACTATTCGGAACATCAAGGTCGCGCGGGTTCTCATTGACGGTGGCAGCT

Reverse complement sequence

AGCTGCCACCGTCAATGAGAACCCGCGCGACCTTGATGTTCCGAATAGTGGGCTCGACCACGATCGGATAGCGTCCTGGGATAACGGCAGTCTTGGGATG[C/G]
TCTTCTTCCGAAAATTCTATCTTCTGTTCAGACCACTTCATATTAGGTGCAGCCCCCTGCCATGTCGAACAGACTTCACGTTCCACTTTCTTGTATTCTC

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	77.60%	21.60%	0.15%	0.63%	NA
All Indica	2759	94.50%	4.30%	0.14%	1.05%	NA
All Japonica	1512	42.40%	57.40%	0.13%	0.07%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	97.50%	2.40%	0.17%	0.00%	NA
Indica II	465	92.50%	4.90%	0.22%	2.37%	NA
Indica III	913	95.10%	4.10%	0.00%	0.88%	NA
Indica Intermediate	786	92.70%	5.70%	0.25%	1.27%	NA
Temperate Japonica	767	4.70%	95.00%	0.13%	0.13%	NA
Tropical Japonica	504	89.50%	10.50%	0.00%	0.00%	NA
Japonica Intermediate	241	63.90%	35.70%	0.41%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	76.70%	22.20%	1.11%	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
vg0801870143	G -> C	LOC_Os08g03930.1	missense_variant ; p.Glu724Asp; MODERATE	nonsynonymous_codon ; E724D	Average:55.052; most accessible tissue: Minghui63 flag leaf, score: 75.722	possibly damaging	-1.59	TOLERATED	1.00
vg0801870143	G -> DEL	LOC_Os08g03930.1	N	frameshift_variant	Average:55.052; most accessible tissue: Minghui63 flag leaf, score: 75.722	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801870143	NA	1.39E-08	mr1368	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
vg0801870143	NA	4.64E-07	mr1551	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
vg0801870143	NA	3.05E-08	mr1584	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
vg0801870143	NA	2.51E-10	mr1593	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
vg0801870143	NA	1.04E-06	mr1942	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
vg0801870143	NA	4.30E-11	mr1216_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
vg0801870143	NA	4.20E-06	mr1263_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
vg0801870143	NA	1.39E-09	mr1350_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
vg0801870143	NA	1.44E-10	mr1368_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
vg0801870143	3.92E-06	1.26E-07	mr1663_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
vg0801870143	NA	3.87E-06	mr1738_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
vg0801870143	NA	6.15E-06	mr1840_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
vg0801870143	NA	5.71E-10	mr1952_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
vg0801870143	NA	1.45E-08	mr1952_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