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Detailed information for vg1003305174:

Variant ID: vg1003305174 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3305174
Reference Allele: T	Alternative Allele: C,G
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGTTGCCTTGGTCATTTGCAATGGCTTGCAGAAGTTGGGTTTGAGTGGCCATAACTCCGGCCAGGGTGGTTAGGTCAGGTGTCTGAGTTTCTTCATTG[T/C,G]
TGGTTGACGCCCGACGTCGGCTTGCCATCTGTGTAGGCCGATTAAGTAAGTATCCTAATTTTCTAACTAGCTCTTGTGGTTTTATCCCATTAAGGGAGTT

Reverse complement sequence

AACTCCCTTAATGGGATAAAACCACAAGAGCTAGTTAGAAAATTAGGATACTTACTTAATCGGCCTACACAGATGGCAAGCCGACGTCGGGCGTCAACCA[A/G,C]
CAATGAAGAAACTCAGACACCTGACCTAACCACCCTGGCCGGAGTTATGGCCACTCAAACCCAACTTCTGCAAGCCATTGCAAATGACCAAGGCAACCGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.30%	33.40%	9.31%	16.97%	NA
All Indica	2759	21.20%	45.60%	12.07%	21.09%	NA
All Japonica	1512	81.40%	2.60%	5.62%	10.32%	NA
Aus	269	4.80%	90.30%	1.86%	2.97%	NA
Indica I	595	42.90%	16.10%	12.77%	28.24%	NA
Indica II	465	14.40%	57.40%	10.54%	17.63%	NA
Indica III	913	9.00%	62.70%	11.72%	16.65%	NA
Indica Intermediate	786	23.20%	41.10%	12.85%	22.90%	NA
Temperate Japonica	767	75.50%	3.30%	6.39%	14.86%	NA
Tropical Japonica	504	89.50%	2.40%	5.56%	2.58%	NA
Japonica Intermediate	241	83.40%	1.20%	3.32%	12.03%	NA
VI/Aromatic	96	33.30%	12.50%	8.33%	45.83%	NA
Intermediate	90	47.80%	28.90%	10.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003305174	T -> C	LOC_Os10g06430.1	missense_variant ; p.Asn221Ser; MODERATE	nonsynonymous_codon	Average:9.525; most accessible tissue: Callus, score: 30.218	benign	-0.962	TOLERATED	0.53
vg1003305174	T -> G	LOC_Os10g06430.1	missense_variant ; p.Asn221Thr; MODERATE	N	Average:9.525; most accessible tissue: Callus, score: 30.218	N	N	N	N
vg1003305174	T -> DEL	LOC_Os10g06430.1	N	frameshift_variant	Average:9.525; most accessible tissue: Callus, score: 30.218	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003305174	NA	9.80E-17	mr1062	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
vg1003305174	NA	1.18E-06	mr1305	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
vg1003305174	NA	1.05E-10	mr1322	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
vg1003305174	NA	5.41E-07	mr1527	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
vg1003305174	NA	7.63E-10	mr1585	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
vg1003305174	NA	7.62E-06	mr1586	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
vg1003305174	NA	2.82E-12	mr1623	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
vg1003305174	NA	5.84E-19	mr1062_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
vg1003305174	NA	1.88E-06	mr1227_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
vg1003305174	NA	7.05E-08	mr1585_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
vg1003305174	NA	3.56E-06	mr1585_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
vg1003305174	NA	7.52E-13	mr1666_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
vg1003305174	NA	3.07E-16	mr1709_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
vg1003305174	NA	4.13E-08	mr1749_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
vg1003305174	NA	1.84E-13	mr1761_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
vg1003305174	NA	2.31E-10	mr1765_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
vg1003305174	NA	1.50E-09	mr1821_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