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Detailed information for vg0430745099:

Variant ID: vg0430745099 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30745099
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, C: 0.04, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

ACGTACGCCACGCAATCGACATGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCTAGGTGTATACGGAAAGTCGAAAGATACACTGGAA[G/C]
CACGTAATGATCTAAAGCATATGGAACAACGCGACGACCTTCACCCGGAACCAAAGGAGAAAGGAAGCCATTACTTGAGTCCAGCCAGCTACACTCTTAG

Reverse complement sequence

CTAAGAGTGTAGCTGGCTGGACTCAAGTAATGGCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGTCGCGTTGTTCCATATGCTTTAGATCATTACGTG[C/G]
TTCCAGTGTATCTTTCGACTTTCCGTATACACCTAGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCATGTCGATTGCGTGGCGTACGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.00%	41.60%	2.77%	1.59%	NA
All Indica	2759	28.50%	69.60%	1.78%	0.14%	NA
All Japonica	1512	89.40%	0.90%	5.09%	4.70%	NA
Aus	269	93.70%	5.90%	0.37%	0.00%	NA
Indica I	595	4.40%	93.60%	2.02%	0.00%	NA
Indica II	465	75.90%	23.90%	0.22%	0.00%	NA
Indica III	913	17.60%	78.90%	3.29%	0.22%	NA
Indica Intermediate	786	31.40%	67.60%	0.76%	0.25%	NA
Temperate Japonica	767	81.60%	0.30%	9.26%	8.87%	NA
Tropical Japonica	504	97.80%	1.60%	0.60%	0.00%	NA
Japonica Intermediate	241	96.30%	1.20%	1.24%	1.24%	NA
VI/Aromatic	96	94.80%	1.00%	4.17%	0.00%	NA
Intermediate	90	80.00%	20.00%	0.00%	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
vg0430745099	G -> C	LOC_Os04g51840.1	missense_variant ; p.Ala205Pro; MODERATE	nonsynonymous_codon ; A205P	Average:21.723; most accessible tissue: Minghui63 young leaf, score: 36.684	possibly damaging	1.702	DELETERIOUS	0.01
vg0430745099	G -> DEL	LOC_Os04g51840.1	N	frameshift_variant	Average:21.723; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430745099	NA	1.18E-16	Grain_length	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0430745099	NA	2.24E-06	mr1050	Ind_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
vg0430745099	NA	1.92E-07	mr1059	Ind_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
vg0430745099	NA	8.19E-07	mr1169	Ind_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
vg0430745099	NA	2.06E-13	mr1531	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
vg0430745099	NA	2.37E-19	mr1598	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
vg0430745099	NA	5.94E-09	mr1629	Ind_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
vg0430745099	NA	1.73E-06	mr1780	Ind_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
vg0430745099	NA	6.70E-08	mr1860	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
vg0430745099	NA	1.12E-06	mr1887	Ind_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
vg0430745099	NA	9.16E-08	mr1321_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
vg0430745099	NA	4.79E-10	mr1349_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
vg0430745099	NA	8.52E-32	mr1598_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