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Detailed information for vg0408293903:

Variant ID: vg0408293903 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8293903
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGAGAAAACCCTTCGCGGAGGAACTCGAGGTGCAGCTGCGGACGATGATCTCGTATGCAAGCCAACACATGCCCCCCGGCATATCGGCTTGACCGACGA[C/T]
ACTCCTGCTTCAAGGCTTCGTCGATACGTTGACCGATGCCTTCGAGCTGGGTGCAGGCGCCATTCAGCCACGAGATATATCCGGCCGCCGATTCCTCAGG

Reverse complement sequence

CCTGAGGAATCGGCGGCCGGATATATCTCGTGGCTGAATGGCGCCTGCACCCAGCTCGAAGGCATCGGTCAACGTATCGACGAAGCCTTGAAGCAGGAGT[G/A]
TCGTCGGTCAAGCCGATATGCCGGGGGGCATGTGTTGGCTTGCATACGAGATCATCGTCCGCAGCTGCACCTCGAGTTCCTCCGCGAAGGGTTTTCTCGT

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	38.40%	2.30%	5.71%	53.60%	NA
All Indica	2759	13.20%	0.10%	7.00%	79.70%	NA
All Japonica	1512	80.00%	6.60%	3.31%	10.12%	NA
Aus	269	45.00%	0.00%	4.09%	50.93%	NA
Indica I	595	4.00%	0.00%	5.55%	90.42%	NA
Indica II	465	36.60%	0.20%	8.17%	55.05%	NA
Indica III	913	8.90%	0.10%	8.21%	82.80%	NA
Indica Intermediate	786	11.30%	0.10%	5.98%	82.57%	NA
Temperate Japonica	767	97.30%	0.00%	0.26%	2.48%	NA
Tropical Japonica	504	53.40%	19.80%	7.94%	18.85%	NA
Japonica Intermediate	241	80.50%	0.00%	3.32%	16.18%	NA
VI/Aromatic	96	74.00%	0.00%	9.38%	16.67%	NA
Intermediate	90	53.30%	7.80%	7.78%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408293903	C -> DEL	LOC_Os04g14780.1	N	frameshift_variant	Average:22.946; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0408293903	C -> T	LOC_Os04g14780.1	missense_variant ; p.Cys497Tyr; MODERATE	nonsynonymous_codon ; C497Y	Average:22.946; most accessible tissue: Minghui63 panicle, score: 42.799	probably damaging	2.244	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408293903	1.10E-06	NA	mr1016	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
vg0408293903	8.94E-07	NA	mr1017	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
vg0408293903	7.24E-06	NA	mr1019	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
vg0408293903	1.73E-07	NA	mr1055	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
vg0408293903	NA	8.22E-07	mr1136	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
vg0408293903	7.55E-06	NA	mr1390	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
vg0408293903	NA	1.34E-06	mr1422	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
vg0408293903	NA	1.11E-07	mr1583	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
vg0408293903	1.69E-06	NA	mr1019_2	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
vg0408293903	1.24E-07	NA	mr1023_2	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
vg0408293903	5.89E-09	NA	mr1055_2	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
vg0408293903	6.54E-07	NA	mr1079_2	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
vg0408293903	1.87E-09	NA	mr1132_2	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
vg0408293903	1.25E-08	NA	mr1390_2	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
vg0408293903	1.54E-06	NA	mr1489_2	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
vg0408293903	6.50E-09	NA	mr1490_2	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