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Detailed information for vg1000738126:

Variant ID: vg1000738126 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 738126
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: 340. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGGTTTATGACTAGTTCAGAATCCCCTTCATACTCCAAGTGCAGCTGCAGCTCTTATCCCAGCGAGTAGTCCTTCATACTCGGCTGTGTTGTTGGTCG[C/T]
CCTGAAGTTAAGGTGAATTGCATGCTTGAACTGATCTCCCGAAGGTGATGTCAAGATGAACCCCGCACCTGCTCCTTGGCTGTTGAGCGCGCCATCGAAA

Reverse complement sequence

TTTCGATGGCGCGCTCAACAGCCAAGGAGCAGGTGCGGGGTTCATCTTGACATCACCTTCGGGAGATCAGTTCAAGCATGCAATTCACCTTAACTTCAGG[G/A]
CGACCAACAACACAGCCGAGTATGAAGGACTACTCGCTGGGATAAGAGCTGCAGCTGCACTTGGAGTATGAAGGGGATTCTGAACTAGTCATAAACCAGG

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	66.60%	5.50%	4.70%	23.17%	NA
All Indica	2759	61.40%	1.10%	3.95%	33.64%	NA
All Japonica	1512	76.80%	6.50%	7.14%	9.59%	NA
Aus	269	68.40%	31.60%	0.00%	0.00%	NA
Indica I	595	70.80%	0.00%	3.53%	25.71%	NA
Indica II	465	39.60%	0.20%	7.10%	53.12%	NA
Indica III	913	62.90%	0.80%	4.05%	32.31%	NA
Indica Intermediate	786	65.40%	2.70%	2.29%	29.64%	NA
Temperate Japonica	767	83.20%	9.30%	4.04%	3.52%	NA
Tropical Japonica	504	69.60%	0.80%	11.71%	17.86%	NA
Japonica Intermediate	241	71.40%	9.50%	7.47%	11.62%	NA
VI/Aromatic	96	55.20%	44.80%	0.00%	0.00%	NA
Intermediate	90	63.30%	6.70%	5.56%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000738126	C -> T	LOC_Os10g02160.1	missense_variant ; p.Ala298Thr; MODERATE	nonsynonymous_codon ; A298T	Average:27.251; most accessible tissue: Zhenshan97 flag leaf, score: 60.705	possibly damaging	1.794	DELETERIOUS	0.03
vg1000738126	C -> DEL	LOC_Os10g02160.1	N	frameshift_variant	Average:27.251; most accessible tissue: Zhenshan97 flag leaf, score: 60.705	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000738126	NA	1.21E-06	mr1040	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
vg1000738126	2.52E-07	NA	mr1310	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
vg1000738126	4.61E-06	NA	mr1549	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
vg1000738126	5.97E-06	3.72E-09	mr1549	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
vg1000738126	NA	4.47E-06	mr1550	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
vg1000738126	5.85E-09	NA	mr1757	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
vg1000738126	3.30E-07	5.52E-12	mr1757	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
vg1000738126	1.26E-08	NA	mr1926	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
vg1000738126	NA	1.64E-06	mr1968	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
vg1000738126	6.76E-13	NA	mr1310_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
vg1000738126	8.28E-10	NA	mr1310_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
vg1000738126	NA	1.48E-08	mr1549_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
vg1000738126	NA	1.55E-06	mr1550_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
vg1000738126	NA	8.51E-07	mr1567_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
vg1000738126	9.06E-07	NA	mr1757_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
vg1000738126	NA	1.80E-08	mr1757_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
vg1000738126	5.12E-07	NA	mr1959_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
vg1000738126	NA	1.30E-06	mr1968_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