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Detailed information for vg0142999785:

Variant ID: vg0142999785 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42999785
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGAGGATAACAGGGGCGGCCTTCCCACAGTGGCTTCGGGGCCGTCCTGGGGGTCGGGGGCTCCTGGCGTCGTCGGACAAGCGGGCAAAGGGCCAACTC[C/T]
GGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCCCGGGTCGAGTCAGCACAGGGTTAGCCTCGGGGTCAAAGGGC

Reverse complement sequence

GCCCTTTGACCCCGAGGCTAACCCTGTGCTGACTCGACCCGGGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACC[G/A]
GAGTTGGCCCTTTGCCCGCTTGTCCGACGACGCCAGGAGCCCCCGACCCCCAGGACGGCCCCGAAGCCACTGTGGGAAGGCCGCCCCTGTTATCCTCCGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 7.50% 0.10% 3.91% 88.47% NA
All Indica  2759 1.10% 0.20% 4.35% 94.35% NA
All Japonica  1512 20.00% 0.00% 0.66% 79.30% NA
Aus  269 3.30% 0.00% 19.33% 77.32% NA
Indica I  595 1.00% 0.00% 2.18% 96.81% NA
Indica II  465 0.20% 0.00% 1.72% 98.06% NA
Indica III  913 1.40% 0.30% 6.79% 91.46% NA
Indica Intermediate  786 1.40% 0.30% 4.71% 93.64% NA
Temperate Japonica  767 37.70% 0.00% 1.17% 61.15% NA
Tropical Japonica  504 1.00% 0.00% 0.20% 98.81% NA
Japonica Intermediate  241 3.70% 0.00% 0.00% 96.27% NA
VI/Aromatic  96 0.00% 0.00% 1.04% 98.96% NA
Intermediate  90 13.30% 0.00% 2.22% 84.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0142999785 C -> T LOC_Os01g74230.1 missense_variant ; p.Gly1073Arg; MODERATE nonsynonymous_codon ; G1073R Average:5.12; most accessible tissue: Zhenshan97 flower, score: 9.663 benign 1.14 TOLERATED 0.08
vg0142999785 C -> DEL LOC_Os01g74230.1 N frameshift_variant Average:5.12; most accessible tissue: Zhenshan97 flower, score: 9.663 N N N N