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Detailed information for vg0709154489:

Variant ID: vg0709154489 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9154489
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCGCGGCCTCGGCGTGCCGGCCGCCGCCGCCGCCGAGGCCGAGCCCGGCGTCCAGGTCGGGCCGTTCGCCGAGGGAGACGTCGAACGTGAGCCCGCCG[G/C]
CGCCGGTGTTCCTCCTGAACAGCGACGGCGGCGCCACGACGCCGTCGTACGGCGGCTGCCGATGATGCATCCCGGCGGCGGCAGCAACGGGCGACGGCGG

Reverse complement sequence

CCGCCGTCGCCCGTTGCTGCCGCCGCCGGGATGCATCATCGGCAGCCGCCGTACGACGGCGTCGTGGCGCCGCCGTCGCTGTTCAGGAGGAACACCGGCG[C/G]
CGGCGGGCTCACGTTCGACGTCTCCCTCGGCGAACGGCCCGACCTGGACGCCGGGCTCGGCCTCGGCGGCGGCGGCGGCCGGCACGCCGAGGCCGCGGCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.20%	9.40%	0.21%	3.22%	NA
All Indica	2759	79.10%	15.90%	0.36%	4.64%	NA
All Japonica	1512	98.40%	0.00%	0.00%	1.59%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	33.60%	51.40%	1.18%	13.78%	NA
Indica II	465	92.90%	6.00%	0.00%	1.08%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	81.40%	13.00%	0.38%	5.22%	NA
Temperate Japonica	767	97.80%	0.00%	0.00%	2.22%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	0.00%	0.00%	2.90%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	0.00%	NA

QTN in RiceNavi

Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.

Category	Variant ID	Chrom	Pos	Gene	MSU	RAP	Alt_Allele_Function	Ref_geno	Alt_geno
Heading date	vg0709154489	Chr7	9154489	Ghd7/Hd4	LOC_Os07g15770	Os07g0261200	promoting heading date under LD	G	C

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709154489	G -> DEL	LOC_Os07g15770.1	N	frameshift_variant	Average:50.431; most accessible tissue: Minghui63 young leaf, score: 79.549	N	N	N	N
vg0709154489	G -> C	LOC_Os07g15770.1	missense_variant ; p.Ala141Gly; MODERATE	nonsynonymous_codon ; A141G	Average:50.431; most accessible tissue: Minghui63 young leaf, score: 79.549	unknown	unknown	TOLERATED	1.00