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Detailed information for vg0424682646:

Variant ID: vg0424682646 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24682646
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 445. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGCATCGACACGAACAGCGCTGTTTTGGTTCGTGCTCTTCATGTCTTGGGCTCTCGTGTAGAATGTGTACCCATTGATCTCATATCCCTGGAATGTCG[C/T]
GATCGACCCAGACGGTCCCCTCGCCAGGAAGGCAAGTTGTTGGTTGATCGACTCGTTACCCATGAGATGTTGTCGTAGCCACGCGAGGAAAGTATCAATG

Reverse complement sequence

CATTGATACTTTCCTCGCGTGGCTACGACAACATCTCATGGGTAACGAGTCGATCAACCAACAACTTGCCTTCCTGGCGAGGGGACCGTCTGGGTCGATC[G/A]
CGACATTCCAGGGATATGAGATCAATGGGTACACATTCTACACGAGAGCCCAAGACATGAAGAGCACGAACCAAAACAGCGCTGTTCGTGTCGATGCCAT

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 69.00% 0.10% 22.07% 8.82% NA
All Indica  2759 49.20% 0.10% 36.82% 13.92% NA
All Japonica  1512 99.60% 0.20% 0.13% 0.07% NA
Aus  269 85.50% 0.00% 4.83% 9.67% NA
Indica I  595 38.30% 0.00% 55.29% 6.39% NA
Indica II  465 40.40% 0.00% 44.52% 15.05% NA
Indica III  913 62.80% 0.20% 19.61% 17.42% NA
Indica Intermediate  786 46.80% 0.00% 38.30% 14.89% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.20% 0.20% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 80.00% 0.00% 13.33% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0424682646 C -> DEL N N silent_mutation Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0424682646 C -> T LOC_Os04g41599.1 intron_variant ; MODIFIER silent_mutation Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N