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Detailed information for vg1214648997:

Variant ID: vg1214648997 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14648997
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGGCCTAAAATAGAGCCCGTCACAGATGACTACTCACCTCAATCGGGCCTAAACTAGAGCCCGTCACAGATGACTACTGACCTCAATCGGGCCTTCCTG[T/C]
TCTTCTTCATCGGTGGGGGTTCATGAATCGCCTTGCTGTCGGCCTCCGTTTGGTCCTCCCCAAAATCCGTGTCGTACTGCAACTGCACATCGTAAGATTG

Reverse complement sequence

CAATCTTACGATGTGCAGTTGCAGTACGACACGGATTTTGGGGAGGACCAAACGGAGGCCGACAGCAAGGCGATTCATGAACCCCCACCGATGAAGAAGA[A/G]
CAGGAAGGCCCGATTGAGGTCAGTAGTCATCTGTGACGGGCTCTAGTTTAGGCCCGATTGAGGTGAGTAGTCATCTGTGACGGGCTCTATTTTAGGCCCG

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	71.30%	10.40%	0.93%	17.35%	NA
All Indica	2759	69.60%	0.90%	0.43%	29.10%	NA
All Japonica	1512	68.10%	29.70%	1.98%	0.26%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	79.30%	0.50%	0.34%	19.83%	NA
Indica II	465	67.70%	0.90%	1.08%	30.32%	NA
Indica III	913	61.40%	0.20%	0.00%	38.34%	NA
Indica Intermediate	786	72.60%	2.00%	0.64%	24.68%	NA
Temperate Japonica	767	43.40%	53.10%	3.13%	0.39%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	82.20%	14.90%	2.49%	0.41%	NA
VI/Aromatic	96	90.60%	0.00%	0.00%	9.38%	NA
Intermediate	90	75.60%	18.90%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214648997	T -> C	LOC_Os12g25390.1	missense_variant ; p.Asn449Ser; MODERATE	nonsynonymous_codon	Average:43.835; most accessible tissue: Minghui63 young leaf, score: 71.839	unknown	unknown	TOLERATED	1.00
vg1214648997	T -> DEL	LOC_Os12g25390.1	N	frameshift_variant	Average:43.835; most accessible tissue: Minghui63 young leaf, score: 71.839	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214648997	5.22E-06	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
vg1214648997	1.01E-08	NA	mr1926	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
vg1214648997	NA	1.86E-07	mr1926	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
vg1214648997	NA	4.75E-11	mr1959	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
vg1214648997	9.13E-07	NA	mr1238_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
vg1214648997	9.77E-09	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
vg1214648997	1.11E-07	NA	mr1484_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
vg1214648997	2.81E-06	NA	mr1609_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
vg1214648997	5.44E-06	5.44E-06	mr1609_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
vg1214648997	1.21E-06	NA	mr1841_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
vg1214648997	2.85E-06	NA	mr1900_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
vg1214648997	4.20E-06	NA	mr1945_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
vg1214648997	6.22E-08	4.35E-17	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
vg1214648997	NA	8.78E-08	mr1959_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