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Detailed information for vg0526045307:

Variant ID: vg0526045307 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 26045307
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTAGTCTTCCTTACACTCTTCTAAATTCCTTTTAGTCAACTTCAATCTGAATATCAATATTCTTCCACATATTTGACGTATTGTATCAGGAATCATAT[C/T]
AATTTGTCCATTCTGTTCCTCCAGCATGGTGGACACAGACTTATGACCAAATATTCTTTCTGCTTCCTCATTAAATATTGTACATGTCGTCCTAGTAGTG

Reverse complement sequence

CACTACTAGGACGACATGTACAATATTTAATGAGGAAGCAGAAAGAATATTTGGTCATAAGTCTGTGTCCACCATGCTGGAGGAACAGAATGGACAAATT[G/A]
ATATGATTCCTGATACAATACGTCAAATATGTGGAAGAATATTGATATTCAGATTGAAGTTGACTAAAAGGAATTTAGAAGAGTGTAAGGAAGACTACAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.30%	3.90%	2.31%	39.53%	NA
All Indica	2759	30.70%	6.70%	3.37%	59.26%	NA
All Japonica	1512	99.30%	0.00%	0.00%	0.66%	NA
Aus	269	21.90%	0.00%	5.20%	72.86%	NA
Indica I	595	27.10%	23.20%	5.04%	44.71%	NA
Indica II	465	29.50%	0.40%	2.80%	67.31%	NA
Indica III	913	31.90%	0.30%	3.29%	64.51%	NA
Indica Intermediate	786	32.70%	5.30%	2.54%	59.41%	NA
Temperate Japonica	767	98.80%	0.00%	0.00%	1.17%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	0.00%	2.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0526045307	C -> T	LOC_Os05g44792.1	missense_variant ; p.Asp737Asn; MODERATE	nonsynonymous_codon ; D737N	Average:7.598; most accessible tissue: Zhenshan97 root, score: 15.132	unknown	unknown	DELETERIOUS	0.00
vg0526045307	C -> DEL	LOC_Os05g44792.1	N	frameshift_variant	Average:7.598; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0526045307	NA	3.46E-06	mr1038	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
vg0526045307	NA	5.19E-07	mr1280	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
vg0526045307	NA	9.60E-06	mr1289	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
vg0526045307	6.62E-06	NA	mr1348	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
vg0526045307	3.46E-06	3.46E-06	mr1348	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
vg0526045307	NA	3.57E-08	mr1389	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
vg0526045307	NA	7.88E-08	mr1389	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
vg0526045307	NA	1.24E-07	mr1571	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
vg0526045307	NA	4.39E-07	mr1881	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
vg0526045307	5.59E-06	5.58E-06	mr1939	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
vg0526045307	NA	1.54E-06	mr1038_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
vg0526045307	NA	1.49E-06	mr1389_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
vg0526045307	NA	5.65E-07	mr1389_2	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