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Detailed information for vg0719013107:

Variant ID: vg0719013107 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19013107
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.30, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTGGGCAACAAGACGTCGATGGAACAGCGGTCTTTCGCACCCCCCAGCAGAACGCGGTTGCAGCAATCACTCTCCTCGACACCCTCCTCAAGGAAGA[T/C]
GCACTCAACCAAGCCGATCATGTTGTCAACATCTTGAACCAGACGAAGACCATGATCGCTGCCTCGGTTCCAGCCAACTCTGCAAGCACCCGTACCCCGA

Reverse complement sequence

TCGGGGTACGGGTGCTTGCAGAGTTGGCTGGAACCGAGGCAGCGATCATGGTCTTCGTCTGGTTCAAGATGTTGACAACATGATCGGCTTGGTTGAGTGC[A/G]
TCTTCCTTGAGGAGGGTGTCGAGGAGAGTGATTGCTGCAACCGCGTTCTGCTGGGGGGTGCGAAAGACCGCTGTTCCATCGACGTCTTGTTGCCCAATGA

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	28.50%	24.50%	30.05%	16.95%	NA
All Indica	2759	41.40%	2.80%	47.84%	8.01%	NA
All Japonica	1512	0.30%	68.50%	1.52%	29.70%	NA
Aus	269	69.50%	0.40%	10.41%	19.70%	NA
Indica I	595	29.70%	1.30%	55.63%	13.28%	NA
Indica II	465	29.70%	3.20%	56.56%	10.54%	NA
Indica III	913	56.00%	2.50%	38.34%	3.18%	NA
Indica Intermediate	786	40.10%	3.90%	47.84%	8.14%	NA
Temperate Japonica	767	0.40%	95.60%	0.65%	3.39%	NA
Tropical Japonica	504	0.00%	31.50%	2.38%	66.07%	NA
Japonica Intermediate	241	0.40%	59.80%	2.49%	37.34%	NA
VI/Aromatic	96	1.00%	19.80%	18.75%	60.42%	NA
Intermediate	90	14.40%	28.90%	34.44%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719013107	T -> DEL	N	N	silent_mutation	Average:10.826; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg0719013107	T -> C	LOC_Os07g31960.1	upstream_gene_variant ; 3462.0bp to feature; MODIFIER	silent_mutation	Average:10.826; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N
vg0719013107	T -> C	LOC_Os07g31960-LOC_Os07g31980	intergenic_region ; MODIFIER	silent_mutation	Average:10.826; most accessible tissue: Minghui63 young leaf, score: 20.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719013107	NA	3.70E-07	mr1044	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
vg0719013107	2.63E-06	NA	mr1107	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
vg0719013107	7.58E-06	NA	mr1145	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
vg0719013107	3.15E-08	2.48E-34	mr1213	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
vg0719013107	NA	4.36E-12	mr1233	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
vg0719013107	NA	1.66E-06	mr1285	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
vg0719013107	2.03E-07	NA	mr1404	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
vg0719013107	NA	3.38E-07	mr1408	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
vg0719013107	1.12E-07	NA	mr1620	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
vg0719013107	NA	6.13E-10	mr1663	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
vg0719013107	6.09E-06	9.82E-18	mr1740	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
vg0719013107	NA	7.00E-06	mr1740	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
vg0719013107	NA	5.45E-13	mr1741	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
vg0719013107	NA	6.81E-10	mr1746	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
vg0719013107	NA	1.45E-07	mr1763	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
vg0719013107	NA	3.15E-15	mr1949	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
vg0719013107	7.16E-08	1.21E-26	mr1233_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
vg0719013107	7.94E-07	NA	mr1620_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
vg0719013107	4.58E-06	2.58E-23	mr1949_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